^DATABASE = GeoMiame
!Database_name = Gene Expression Omnibus (GEO)
!Database_institute = NCBI NLM NIH
!Database_web_link = http://www.ncbi.nlm.nih.gov/geo
!Database_email = geo@ncbi.nlm.nih.gov
^SERIES = GSE107011
!Series_title = RNA-Seq profiling of 29 immune cell types and peripheral blood mononuclear cells
!Series_geo_accession = GSE107011
!Series_status = Public on Feb 06 2019
!Series_submission_date = Nov 16 2017
!Series_last_update_date = Jul 08 2021
!Series_pubmed_id = 30528453
!Series_pubmed_id = 30726743
!Series_pubmed_id = 34010947
!Series_summary = We performed RNA-Seq transcriptome profiling on 29 immune cell types consituting peripheral blood mononuclear cells (PBMCs) sorted from 4 Singaporean-Chinese individuals (S4 cohort). We also performed RNA-Seq and microarray transcriptome profiling of PBMCs from an extended cohort of 13 individuals (S13 cohort). The data was used first to characterize the transcriptomic signatures and relationships among the 29 immune cell types. Then we explored the difference in mRNA composition in terms of transcripts proportions and abundance. Lastly, we performed deep deconvolution for both microarray and RNA-Seq technologies.
!Series_overall_design = Total RNA of 29 immune cell types (from 4 individuals) and peripheral blood mononuclear cells (PBMCs, from 13 individuals) was extracted for gene expression profiling. The 13 PBMCs samples were processed with both microarray and RNA-Seq platforms.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Gianni,,Monaco
!Series_contributor = Bernett,,Lee
!Series_contributor = Weili,,Xu
!Series_contributor = You,,Hwang
!Series_contributor = Michael,,Poidinger
!Series_contributor = Michael,,Poidinger
!Series_contributor = João,,de Magalhães
!Series_contributor = Anis,,Larbi
!Series_sample_id = GSM2859411
!Series_sample_id = GSM2859412
!Series_sample_id = GSM2859413
!Series_sample_id = GSM2859414
!Series_sample_id = GSM2859415
!Series_sample_id = GSM2859416
!Series_sample_id = GSM2859417
!Series_sample_id = GSM2859418
!Series_sample_id = GSM2859419
!Series_sample_id = GSM2859420
!Series_sample_id = GSM2859421
!Series_sample_id = GSM2859422
!Series_sample_id = GSM2859423
!Series_sample_id = GSM2859424
!Series_sample_id = GSM2859425
!Series_sample_id = GSM2859426
!Series_sample_id = GSM2859427
!Series_sample_id = GSM2859428
!Series_sample_id = GSM2859429
!Series_sample_id = GSM2859430
!Series_sample_id = GSM2859431
!Series_sample_id = GSM2859432
!Series_sample_id = GSM2859433
!Series_sample_id = GSM2859434
!Series_sample_id = GSM2859435
!Series_sample_id = GSM2859436
!Series_sample_id = GSM2859437
!Series_sample_id = GSM2859438
!Series_sample_id = GSM2859439
!Series_sample_id = GSM2859440
!Series_sample_id = GSM2859441
!Series_sample_id = GSM2859442
!Series_sample_id = GSM2859443
!Series_sample_id = GSM2859444
!Series_sample_id = GSM2859445
!Series_sample_id = GSM2859446
!Series_sample_id = GSM2859447
!Series_sample_id = GSM2859448
!Series_sample_id = GSM2859449
!Series_sample_id = GSM2859450
!Series_sample_id = GSM2859451
!Series_sample_id = GSM2859452
!Series_sample_id = GSM2859453
!Series_sample_id = GSM2859454
!Series_sample_id = GSM2859455
!Series_sample_id = GSM2859456
!Series_sample_id = GSM2859457
!Series_sample_id = GSM2859458
!Series_sample_id = GSM2859459
!Series_sample_id = GSM2859460
!Series_sample_id = GSM2859461
!Series_sample_id = GSM2859462
!Series_sample_id = GSM2859463
!Series_sample_id = GSM2859464
!Series_sample_id = GSM2859465
!Series_sample_id = GSM2859466
!Series_sample_id = GSM2859467
!Series_sample_id = GSM2859468
!Series_sample_id = GSM2859469
!Series_sample_id = GSM2859470
!Series_sample_id = GSM2859471
!Series_sample_id = GSM2859472
!Series_sample_id = GSM2859473
!Series_sample_id = GSM2859474
!Series_sample_id = GSM2859475
!Series_sample_id = GSM2859476
!Series_sample_id = GSM2859477
!Series_sample_id = GSM2859478
!Series_sample_id = GSM2859479
!Series_sample_id = GSM2859480
!Series_sample_id = GSM2859481
!Series_sample_id = GSM2859482
!Series_sample_id = GSM2859483
!Series_sample_id = GSM2859484
!Series_sample_id = GSM2859485
!Series_sample_id = GSM2859486
!Series_sample_id = GSM2859487
!Series_sample_id = GSM2859488
!Series_sample_id = GSM2859489
!Series_sample_id = GSM2859490
!Series_sample_id = GSM2859491
!Series_sample_id = GSM2859492
!Series_sample_id = GSM2859493
!Series_sample_id = GSM2859494
!Series_sample_id = GSM2859495
!Series_sample_id = GSM2859496
!Series_sample_id = GSM2859497
!Series_sample_id = GSM2859498
!Series_sample_id = GSM2859499
!Series_sample_id = GSM2859500
!Series_sample_id = GSM2859501
!Series_sample_id = GSM2859502
!Series_sample_id = GSM2859503
!Series_sample_id = GSM2859504
!Series_sample_id = GSM2859505
!Series_sample_id = GSM2859506
!Series_sample_id = GSM2859507
!Series_sample_id = GSM2859508
!Series_sample_id = GSM2859509
!Series_sample_id = GSM2859510
!Series_sample_id = GSM2859511
!Series_sample_id = GSM2859512
!Series_sample_id = GSM2859513
!Series_sample_id = GSM2859514
!Series_sample_id = GSM2859515
!Series_sample_id = GSM2859516
!Series_sample_id = GSM2859517
!Series_sample_id = GSM2859518
!Series_sample_id = GSM2859519
!Series_sample_id = GSM2859520
!Series_sample_id = GSM2859521
!Series_sample_id = GSM2859522
!Series_sample_id = GSM2859523
!Series_sample_id = GSM2859524
!Series_sample_id = GSM2859525
!Series_sample_id = GSM2859526
!Series_sample_id = GSM2859527
!Series_sample_id = GSM2859528
!Series_sample_id = GSM2859529
!Series_sample_id = GSM2859530
!Series_sample_id = GSM2859531
!Series_sample_id = GSM2859532
!Series_sample_id = GSM2859533
!Series_sample_id = GSM2859534
!Series_sample_id = GSM2859535
!Series_sample_id = GSM2859536
!Series_sample_id = GSM2859537
!Series_contact_name = Gianni,,Monaco
!Series_contact_email = mongianni1@gmail.com
!Series_contact_department = Institute of Neuropathology
!Series_contact_institute = Freiburg Medical Center
!Series_contact_address = Breisacher Straße 64
!Series_contact_city = Freiburg
!Series_contact_zip/postal_code = 79106
!Series_contact_country = Germany
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107011/suppl/GSE107011_Processed_data_TPM.txt.gz
!Series_platform_id = GPL11154
!Series_platform_taxid = 9606
!Series_sample_taxid = 9606
!Series_relation = SubSeries of: GSE107019
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA418779
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP125125
^PLATFORM = GPL11154
!Platform_title = Illumina HiSeq 2000 (Homo sapiens)
!Platform_geo_accession = GPL11154
!Platform_status = Public on Nov 02 2010
!Platform_submission_date = Nov 02 2010
!Platform_last_update_date = Mar 27 2019
!Platform_technology = high-throughput sequencing
!Platform_distribution = virtual
!Platform_organism = Homo sapiens
!Platform_taxid = 9606
!Platform_contact_name = ,,GEO
!Platform_contact_country = USA
!Platform_data_row_count = 0
^SAMPLE = GSM2859411
!Sample_title = DZQV_CD8_naive_rep4
!Sample_geo_accession = GSM2859411
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Naive CD8 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Naive CD8 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 900000
!Sample_description = total_rna_yield (ng): 321.78
!Sample_description = DZQV_CD8_naive
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035215
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399186
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859412
!Sample_title = DZQV_CD8_CM_rep4
!Sample_geo_accession = GSM2859412
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Central memory CD8 T cell
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Central memory CD8 T cell
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 324600
!Sample_description = total_rna_yield (ng): 102.468
!Sample_description = DZQV_CD8_CM
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035214
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399187
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859413
!Sample_title = DZQV_CD8_EM_rep4
!Sample_geo_accession = GSM2859413
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Effector memory CD8 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Effector memory CD8 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 1181147
!Sample_description = total_rna_yield (ng): 488.508
!Sample_description = DZQV_CD8_EM
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035213
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399188
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859414
!Sample_title = DZQV_CD8_TE_rep4
!Sample_geo_accession = GSM2859414
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Terminal effector CD8 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Terminal effector CD8 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 1000000
!Sample_description = total_rna_yield (ng): 274.26
!Sample_description = DZQV_CD8_TE
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035212
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399189
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859415
!Sample_title = DZQV_MAIT_rep4
!Sample_geo_accession = GSM2859415
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = MAIT cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: MAIT cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 900000
!Sample_description = total_rna_yield (ng): 449.82
!Sample_description = DZQV_MAIT
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035211
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399190
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859416
!Sample_title = DZQV_VD2+_rep4
!Sample_geo_accession = GSM2859416
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Vd2 gd T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Vd2 gd T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 900000
!Sample_description = total_rna_yield (ng): 350.424
!Sample_description = DZQV_VD2+
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035256
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399191
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859417
!Sample_title = DZQV_VD2-_rep4
!Sample_geo_accession = GSM2859417
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Non-Vd2 gd T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Non-Vd2 gd T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 1003272
!Sample_description = total_rna_yield (ng): 240.156
!Sample_description = DZQV_VD2-
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035255
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399192
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859418
!Sample_title = DZQV_TFH_rep4
!Sample_geo_accession = GSM2859418
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Follicular helper T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Follicular helper T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 360352
!Sample_description = total_rna_yield (ng): 61.668
!Sample_description = DZQV_TFH
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035254
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399193
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859419
!Sample_title = DZQV_Treg_rep4
!Sample_geo_accession = GSM2859419
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = T regulatory cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: T regulatory cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 170358
!Sample_description = total_rna_yield (ng): 11.58
!Sample_description = DZQV_Treg
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035253
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399194
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859420
!Sample_title = DZQV_Th1_rep4
!Sample_geo_accession = GSM2859420
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Th1 cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Th1 cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 450000
!Sample_description = total_rna_yield (ng): 70.956
!Sample_description = DZQV_Th1
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035252
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399195
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859421
!Sample_title = DZQV_Th1/Th17_rep4
!Sample_geo_accession = GSM2859421
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Th1/Th17 cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Th1/Th17 cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 156343
!Sample_description = total_rna_yield (ng): 23.592
!Sample_description = DZQV_Th1/Th17
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035251
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399196
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859422
!Sample_title = DZQV_Th17_rep4
!Sample_geo_accession = GSM2859422
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Th17 cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Th17 cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 205024
!Sample_description = total_rna_yield (ng): 33.696
!Sample_description = DZQV_Th17
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035250
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399197
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859423
!Sample_title = DZQV_Th2_rep4
!Sample_geo_accession = GSM2859423
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Th2 cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Th2 cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 82465
!Sample_description = total_rna_yield (ng): 8.016
!Sample_description = DZQV_Th2
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035249
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399198
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859424
!Sample_title = DZQV_CD4_naive_rep4
!Sample_geo_accession = GSM2859424
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Naive CD4 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Naive CD4 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 450000
!Sample_description = total_rna_yield (ng): 58.056
!Sample_description = DZQV_CD4_naive
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035248
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399199
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859425
!Sample_title = DZQV_Progenitor_rep4
!Sample_geo_accession = GSM2859425
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Progenitor cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Progenitor cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 74692
!Sample_description = total_rna_yield (ng): 15.024
!Sample_description = DZQV_Progenitor
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035247
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399200
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859426
!Sample_title = DZQV_B_naive_rep4
!Sample_geo_accession = GSM2859426
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Naive B cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Naive B cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 702312
!Sample_description = total_rna_yield (ng): 149.232
!Sample_description = DZQV_B_naive
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035242
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399201
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859427
!Sample_title = DZQV_B_NSM_rep4
!Sample_geo_accession = GSM2859427
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Non-switched memory B cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Non-switched memory B cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 450000
!Sample_description = total_rna_yield (ng): 171.612
!Sample_description = DZQV_B_NSM
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035241
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399202
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859428
!Sample_title = DZQV_B_Ex_rep4
!Sample_geo_accession = GSM2859428
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Exhausted B cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Exhausted B cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 149548
!Sample_description = total_rna_yield (ng): 29.112
!Sample_description = DZQV_B_Ex
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035243
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399203
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859429
!Sample_title = DZQV_B_SM_rep4
!Sample_geo_accession = GSM2859429
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Switched memory B cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Switched memory B cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 450000
!Sample_description = total_rna_yield (ng): 176.736
!Sample_description = DZQV_B_SM
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035244
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399204
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859430
!Sample_title = DZQV_Plasmablasts_rep4
!Sample_geo_accession = GSM2859430
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Plasmablasts
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Plasmablasts
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 291240
!Sample_description = total_rna_yield (ng): 755.112
!Sample_description = DZQV_Plasmablasts
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035245
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399205
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859431
!Sample_title = DZQV_C_mono_rep4
!Sample_geo_accession = GSM2859431
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Classical monocytes
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Classical monocytes
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 300000
!Sample_description = total_rna_yield (ng): 187.476
!Sample_description = DZQV_C_mono
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035246
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399206
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859432
!Sample_title = DZQV_I_mono_rep4
!Sample_geo_accession = GSM2859432
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Intermediate monocytes
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Intermediate monocytes
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 230847
!Sample_description = total_rna_yield (ng): 326.124
!Sample_description = DZQV_I_mono
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035240
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399207
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859433
!Sample_title = DZQV_NC_mono_rep4
!Sample_geo_accession = GSM2859433
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Non classical monocytes
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Non classical monocytes
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 234326
!Sample_description = total_rna_yield (ng): 120.108
!Sample_description = DZQV_NC_mono
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035239
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399208
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859434
!Sample_title = DZQV_NK_rep4
!Sample_geo_accession = GSM2859434
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Natural killer cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Natural killer cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 300000
!Sample_description = total_rna_yield (ng): 104.58
!Sample_description = DZQV_NK
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035238
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399209
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859435
!Sample_title = DZQV_pDC_rep4
!Sample_geo_accession = GSM2859435
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Plasmacytoid dendritic cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Plasmacytoid dendritic cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 200079
!Sample_description = total_rna_yield (ng): 237.228
!Sample_description = DZQV_pDC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035237
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399210
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859436
!Sample_title = DZQV_mDC_rep4
!Sample_geo_accession = GSM2859436
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Myeloid dendritic cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Myeloid dendritic cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 236429
!Sample_description = total_rna_yield (ng): 226.632
!Sample_description = DZQV_mDC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035236
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399211
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859437
!Sample_title = DZQV_Neutrophils_rep4
!Sample_geo_accession = GSM2859437
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Low-density neutrophils
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Low-density neutrophils
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 147334
!Sample_description = total_rna_yield (ng): 5.076
!Sample_description = DZQV_Neutrophils
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035235
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399212
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859438
!Sample_title = DZQV_Basophils_rep4
!Sample_geo_accession = GSM2859438
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Low-density basophils
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Low-density basophils
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 300000
!Sample_description = total_rna_yield (ng): 8.496
!Sample_description = DZQV_Basophils
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035234
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399213
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859439
!Sample_title = 925L_CD8_naive_rep2
!Sample_geo_accession = GSM2859439
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Naive CD8 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Naive CD8 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 400000
!Sample_description = total_rna_yield (ng): 211.392
!Sample_description = 925L_CD8_naive
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035233
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399214
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859440
!Sample_title = 925L_CD8_CM_rep2
!Sample_geo_accession = GSM2859440
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Central memory CD8 T cell
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Central memory CD8 T cell
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 400000
!Sample_description = total_rna_yield (ng): 232.92
!Sample_description = 925L_CD8_CM
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035232
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399215
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859441
!Sample_title = 925L_CD8_EM_rep2
!Sample_geo_accession = GSM2859441
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Effector memory CD8 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Effector memory CD8 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 400000
!Sample_description = total_rna_yield (ng): 159.144
!Sample_description = 925L_CD8_EM
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035231
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399216
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859442
!Sample_title = 925L_CD8_TE_rep2
!Sample_geo_accession = GSM2859442
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Terminal effector CD8 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Terminal effector CD8 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 400000
!Sample_description = total_rna_yield (ng): 138.384
!Sample_description = 925L_CD8_TE
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035230
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399217
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859443
!Sample_title = 925L_MAIT_rep2
!Sample_geo_accession = GSM2859443
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = MAIT cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: MAIT cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 387411
!Sample_description = total_rna_yield (ng): 298.884
!Sample_description = 925L_MAIT
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035229
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399218
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859444
!Sample_title = 925L_VD2+_rep2
!Sample_geo_accession = GSM2859444
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Vd2 gd T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Vd2 gd T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 400000
!Sample_description = total_rna_yield (ng): 331.068
!Sample_description = 925L_VD2+
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035208
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399219
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859445
!Sample_title = 925L_VD2-_rep2
!Sample_geo_accession = GSM2859445
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Non-Vd2 gd T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Non-Vd2 gd T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 295074
!Sample_description = total_rna_yield (ng): 122.46
!Sample_description = 925L_VD2-
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035207
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399220
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859446
!Sample_title = 925L_TFH_rep2
!Sample_geo_accession = GSM2859446
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Follicular helper T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Follicular helper T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 400000
!Sample_description = total_rna_yield (ng): 161.46
!Sample_description = 925L_TFH
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035206
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399221
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859447
!Sample_title = 925L_Treg_rep2
!Sample_geo_accession = GSM2859447
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = T regulatory cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: T regulatory cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 312007
!Sample_description = total_rna_yield (ng): 93.456
!Sample_description = 925L_Treg
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035205
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399222
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859448
!Sample_title = 925L_Th1_rep2
!Sample_geo_accession = GSM2859448
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Th1 cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Th1 cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 444395
!Sample_description = total_rna_yield (ng): 214.788
!Sample_description = 925L_Th1
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035204
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399223
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859449
!Sample_title = 925L_Th1/Th17_rep2
!Sample_geo_accession = GSM2859449
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Th1/Th17 cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Th1/Th17 cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 387451
!Sample_description = total_rna_yield (ng): 203.832
!Sample_description = 925L_Th1/Th17
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035203
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399224
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859450
!Sample_title = 925L_Th17_rep2
!Sample_geo_accession = GSM2859450
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Th17 cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Th17 cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 290254
!Sample_description = total_rna_yield (ng): 165.576
!Sample_description = 925L_Th17
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035202
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399225
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859451
!Sample_title = 925L_Th2_rep2
!Sample_geo_accession = GSM2859451
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Th2 cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Th2 cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 400198
!Sample_description = total_rna_yield (ng): 255.192
!Sample_description = 925L_Th2
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035201
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399226
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859452
!Sample_title = 925L_CD4_naive_rep2
!Sample_geo_accession = GSM2859452
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Naive CD4 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Naive CD4 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 370000
!Sample_description = total_rna_yield (ng): 118.992
!Sample_description = 925L_CD4_naive
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035200
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399227
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859453
!Sample_title = 925L_CD4_TE_rep2
!Sample_geo_accession = GSM2859453
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Terminal effector CD4 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Terminal effector CD4 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 183582
!Sample_description = total_rna_yield (ng): 31.836
!Sample_description = 925L_CD4_TE
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035199
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399228
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859454
!Sample_title = 925L_Progenitor_rep2
!Sample_geo_accession = GSM2859454
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Progenitor cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Progenitor cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 19215
!Sample_description = total_rna_yield (ng): 4.656
!Sample_description = 925L_Progenitor
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035198
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399229
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859455
!Sample_title = 925L_B_naive_rep2
!Sample_geo_accession = GSM2859455
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Naive B cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Naive B cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 2250000
!Sample_description = total_rna_yield (ng): 784.5
!Sample_description = 925L_B_naive
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035197
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399230
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859456
!Sample_title = 925L_B_NSM_rep2
!Sample_geo_accession = GSM2859456
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Non-switched memory B cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Non-switched memory B cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 399587
!Sample_description = total_rna_yield (ng): 123.852
!Sample_description = 925L_B_NSM
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035196
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399231
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859457
!Sample_title = 925L_B_Ex_rep2
!Sample_geo_accession = GSM2859457
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Exhausted B cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Exhausted B cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 52906
!Sample_description = total_rna_yield (ng): 7.752
!Sample_description = 925L_B_Ex
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035195
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399232
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859458
!Sample_title = 925L_B_SM_rep2
!Sample_geo_accession = GSM2859458
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Switched memory B cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Switched memory B cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 564388
!Sample_description = total_rna_yield (ng): 249.9
!Sample_description = 925L_B_SM
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035194
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399233
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859459
!Sample_title = 925L_Plasmablasts_rep2
!Sample_geo_accession = GSM2859459
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Plasmablasts
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Plasmablasts
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 14264
!Sample_description = total_rna_yield (ng): 10.788
!Sample_description = 925L_Plasmablasts
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035193
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399234
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859460
!Sample_title = 925L_C_mono_rep2
!Sample_geo_accession = GSM2859460
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Classical monocytes
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Classical monocytes
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 300000
!Sample_description = total_rna_yield (ng): 160.908
!Sample_description = 925L_C_mono
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035217
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399235
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859461
!Sample_title = 925L_I_mono_rep2
!Sample_geo_accession = GSM2859461
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Intermediate monocytes
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Intermediate monocytes
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 216933
!Sample_description = total_rna_yield (ng): 114.672
!Sample_description = 925L_I_mono
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035192
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399236
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859462
!Sample_title = 925L_NC_mono_rep2
!Sample_geo_accession = GSM2859462
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Non classical monocytes
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Non classical monocytes
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 231932
!Sample_description = total_rna_yield (ng): 153.492
!Sample_description = 925L_NC_mono
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035191
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399237
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859463
!Sample_title = 925L_NK_rep2
!Sample_geo_accession = GSM2859463
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Natural killer cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Natural killer cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 300000
!Sample_description = total_rna_yield (ng): 106.392
!Sample_description = 925L_NK
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035210
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399238
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859464
!Sample_title = 925L_pDC_rep2
!Sample_geo_accession = GSM2859464
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Plasmacytoid dendritic cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Plasmacytoid dendritic cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 35453
!Sample_description = total_rna_yield (ng): 40.176
!Sample_description = 925L_pDC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035209
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399239
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859465
!Sample_title = 925L_mDC_rep2
!Sample_geo_accession = GSM2859465
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Myeloid dendritic cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Myeloid dendritic cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 229213
!Sample_description = total_rna_yield (ng): 363.624
!Sample_description = 925L_mDC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035216
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399240
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859466
!Sample_title = 925L_Neutrophils_rep2
!Sample_geo_accession = GSM2859466
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Low-density neutrophils
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Low-density neutrophils
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 217968
!Sample_description = total_rna_yield (ng): 10.416
!Sample_description = 925L_Neutrophils
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035190
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399241
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859467
!Sample_title = 925L_Basophils_rep2
!Sample_geo_accession = GSM2859467
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Low-density basophils
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Low-density basophils
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 300000
!Sample_description = total_rna_yield (ng): 16.98
!Sample_description = 925L_Basophils
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035189
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399242
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859468
!Sample_title = 9JD4_CD8_naive_rep1
!Sample_geo_accession = GSM2859468
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Naive CD8 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Naive CD8 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 625000
!Sample_description = total_rna_yield (ng): 715.032
!Sample_description = 9JD4_CD8_naive
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035188
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399243
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859469
!Sample_title = 9JD4_CD8_CM_rep1
!Sample_geo_accession = GSM2859469
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Central memory CD8 T cell
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Central memory CD8 T cell
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 351567
!Sample_description = total_rna_yield (ng): 363.48
!Sample_description = 9JD4_CD8_CM
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035187
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399244
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859470
!Sample_title = 9JD4_CD8_EM_rep1
!Sample_geo_accession = GSM2859470
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Effector memory CD8 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Effector memory CD8 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 625744
!Sample_description = total_rna_yield (ng): 409.908
!Sample_description = 9JD4_CD8_EM
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035186
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399245
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859471
!Sample_title = 9JD4_CD8_TE_rep1
!Sample_geo_accession = GSM2859471
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Terminal effector CD8 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Terminal effector CD8 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 625000
!Sample_description = total_rna_yield (ng): 439.32
!Sample_description = 9JD4_CD8_TE
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035185
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399246
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859472
!Sample_title = 9JD4_MAIT_rep1
!Sample_geo_accession = GSM2859472
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = MAIT cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: MAIT cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 625000
!Sample_description = total_rna_yield (ng): 633.516
!Sample_description = 9JD4_MAIT
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035184
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399247
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859473
!Sample_title = 9JD4_VD2+_rep1
!Sample_geo_accession = GSM2859473
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Vd2 gd T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Vd2 gd T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 464891
!Sample_description = total_rna_yield (ng): 409.236
!Sample_description = 9JD4_VD2+
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035183
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399248
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859474
!Sample_title = 9JD4_VD2-_rep1
!Sample_geo_accession = GSM2859474
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Non-Vd2 gd T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Non-Vd2 gd T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 769746
!Sample_description = total_rna_yield (ng): 414.984
!Sample_description = 9JD4_VD2-
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035182
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399249
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859475
!Sample_title = 9JD4_TFH_rep1
!Sample_geo_accession = GSM2859475
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Follicular helper T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Follicular helper T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 716271
!Sample_description = total_rna_yield (ng): 383.016
!Sample_description = 9JD4_TFH
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035181
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399250
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859476
!Sample_title = 9JD4_Treg_rep1
!Sample_geo_accession = GSM2859476
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = T regulatory cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: T regulatory cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 582455
!Sample_description = total_rna_yield (ng): 295.668
!Sample_description = 9JD4_Treg
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035180
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399251
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859477
!Sample_title = 9JD4_Th1_rep1
!Sample_geo_accession = GSM2859477
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Th1 cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Th1 cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 788747
!Sample_description = total_rna_yield (ng): 408.648
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!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035179
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399252
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859478
!Sample_title = 9JD4_Th1/Th17_rep1
!Sample_geo_accession = GSM2859478
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Th1/Th17 cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Th1/Th17 cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 450000
!Sample_description = total_rna_yield (ng): 356.544
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!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035178
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399253
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859479
!Sample_title = 9JD4_Th17_rep1
!Sample_geo_accession = GSM2859479
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Th17 cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Th17 cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 431738
!Sample_description = total_rna_yield (ng): 261.564
!Sample_description = 9JD4_Th17
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035177
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399254
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859480
!Sample_title = 9JD4_Th2_rep1
!Sample_geo_accession = GSM2859480
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Th2 cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Th2 cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 299584
!Sample_description = total_rna_yield (ng): 111.06
!Sample_description = 9JD4_Th2
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035176
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399255
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859481
!Sample_title = 9JD4_CD4_naive_rep1
!Sample_geo_accession = GSM2859481
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Naive CD4 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Naive CD4 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 450000
!Sample_description = total_rna_yield (ng): 193.992
!Sample_description = 9JD4_CD4_naive
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035175
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399256
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859482
!Sample_title = 9JD4_CD4_TE_rep1
!Sample_geo_accession = GSM2859482
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Terminal effector CD4 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Terminal effector CD4 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 114066
!Sample_description = total_rna_yield (ng): 18.984
!Sample_description = 9JD4_CD4_TE
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035174
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399257
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859483
!Sample_title = 9JD4_Progenitor_rep1
!Sample_geo_accession = GSM2859483
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Progenitor cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Progenitor cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 22930
!Sample_description = total_rna_yield (ng): 7.548
!Sample_description = 9JD4_Progenitor
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035173
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399258
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859484
!Sample_title = 9JD4_B_naive_rep1
!Sample_geo_accession = GSM2859484
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Naive B cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Naive B cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 1499746
!Sample_description = total_rna_yield (ng): 705.012
!Sample_description = 9JD4_B_naive
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035172
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399259
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859485
!Sample_title = 9JD4_B_NSM_rep1
!Sample_geo_accession = GSM2859485
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Non-switched memory B cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Non-switched memory B cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 317742
!Sample_description = total_rna_yield (ng): 117.432
!Sample_description = 9JD4_B_NSM
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035171
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399260
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859486
!Sample_title = 9JD4_B_Ex_rep1
!Sample_geo_accession = GSM2859486
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Exhausted B cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Exhausted B cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 122804
!Sample_description = total_rna_yield (ng): 30.18
!Sample_description = 9JD4_B_Ex
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035170
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399261
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859487
!Sample_title = 9JD4_B_SM_rep1
!Sample_geo_accession = GSM2859487
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Switched memory B cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Switched memory B cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 557031
!Sample_description = total_rna_yield (ng): 370.896
!Sample_description = 9JD4_B_SM
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035169
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399262
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859488
!Sample_title = 9JD4_Plasmablasts_rep1
!Sample_geo_accession = GSM2859488
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Plasmablasts
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Plasmablasts
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 61729
!Sample_description = total_rna_yield (ng): 76.2
!Sample_description = 9JD4_Plasmablasts
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035168
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399263
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859489
!Sample_title = 9JD4_C_mono_rep1
!Sample_geo_accession = GSM2859489
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Classical monocytes
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Classical monocytes
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 300000
!Sample_description = total_rna_yield (ng): 258.78
!Sample_description = 9JD4_C_mono
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035167
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399264
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859490
!Sample_title = 9JD4_I_mono_rep1
!Sample_geo_accession = GSM2859490
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Intermediate monocytes
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Intermediate monocytes
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 172399
!Sample_description = total_rna_yield (ng): 169.416
!Sample_description = 9JD4_I_mono
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035166
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399265
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859491
!Sample_title = 9JD4_NC_mono_rep1
!Sample_geo_accession = GSM2859491
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Non classical monocytes
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Non classical monocytes
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 195224
!Sample_description = total_rna_yield (ng): 128.328
!Sample_description = 9JD4_NC_mono
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035165
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399266
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859492
!Sample_title = 9JD4_NK_rep1
!Sample_geo_accession = GSM2859492
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Natural killer cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Natural killer cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 300000
!Sample_description = total_rna_yield (ng): 90.216
!Sample_description = 9JD4_NK
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035164
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399267
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859493
!Sample_title = 9JD4_pDC_rep1
!Sample_geo_accession = GSM2859493
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Plasmacytoid dendritic cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Plasmacytoid dendritic cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 247703
!Sample_description = total_rna_yield (ng): 416.952
!Sample_description = 9JD4_pDC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035163
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399268
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859494
!Sample_title = 9JD4_mDC_rep1
!Sample_geo_accession = GSM2859494
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Myeloid dendritic cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Myeloid dendritic cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 272295
!Sample_description = total_rna_yield (ng): 295.98
!Sample_description = 9JD4_mDC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035162
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399269
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859495
!Sample_title = 9JD4_Neutrophils_rep1
!Sample_geo_accession = GSM2859495
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Low-density neutrophils
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Low-density neutrophils
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 287632
!Sample_description = total_rna_yield (ng): 3.504
!Sample_description = 9JD4_Neutrophils
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035161
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399270
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859496
!Sample_title = 9JD4_Basophils_rep1
!Sample_geo_accession = GSM2859496
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Low-density basophils
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Low-density basophils
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 300000
!Sample_description = total_rna_yield (ng): 8.292
!Sample_description = 9JD4_Basophils
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035160
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399271
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859497
!Sample_title = G4YW_CD8_naive_rep3
!Sample_geo_accession = GSM2859497
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Naive CD8 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Naive CD8 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 300000
!Sample_description = total_rna_yield (ng): 99.768
!Sample_description = G4YW_CD8_naive
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035159
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399272
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859498
!Sample_title = G4YW_CD8_CM_rep3
!Sample_geo_accession = GSM2859498
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Central memory CD8 T cell
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Central memory CD8 T cell
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 232579
!Sample_description = total_rna_yield (ng): 151.032
!Sample_description = G4YW_CD8_CM
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035158
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399273
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859499
!Sample_title = G4YW_CD8_EM_rep3
!Sample_geo_accession = GSM2859499
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Effector memory CD8 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Effector memory CD8 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 391537
!Sample_description = total_rna_yield (ng): 279.036
!Sample_description = G4YW_CD8_EM
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035157
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399274
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859500
!Sample_title = CYFZ_PBMC_rep9
!Sample_geo_accession = GSM2859500
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = PBMCs
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: PBMCs
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 2000000
!Sample_description = total_rna_yield (ng): 3140.412
!Sample_description = CYFZ_PBMC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035156
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399275
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859501
!Sample_title = FY2H_PBMC_rep8
!Sample_geo_accession = GSM2859501
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = PBMCs
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: PBMCs
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 2000000
!Sample_description = total_rna_yield (ng): 4728
!Sample_description = FY2H_PBMC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035155
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399276
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859502
!Sample_title = FLWA_PBMC_rep10
!Sample_geo_accession = GSM2859502
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = PBMCs
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: PBMCs
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 2000000
!Sample_description = total_rna_yield (ng): 3681.588
!Sample_description = FLWA_PBMC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035154
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399277
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859503
!Sample_title = 453W_PBMC_rep5
!Sample_geo_accession = GSM2859503
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = PBMCs
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: PBMCs
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 1000000
!Sample_description = total_rna_yield (ng): 559.32
!Sample_description = 453W_PBMC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035153
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399278
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859504
!Sample_title = 684C_PBMC_rep6
!Sample_geo_accession = GSM2859504
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = PBMCs
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: PBMCs
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 1000000
!Sample_description = total_rna_yield (ng): 530.076
!Sample_description = 684C_PBMC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035152
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399279
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859505
!Sample_title = CZJE_PBMC_rep7
!Sample_geo_accession = GSM2859505
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = PBMCs
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: PBMCs
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 1000000
!Sample_description = total_rna_yield (ng): 560.292
!Sample_description = CZJE_PBMC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035151
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399280
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859506
!Sample_title = G4YW_CD8_TE_rep3
!Sample_geo_accession = GSM2859506
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Terminal effector CD8 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Terminal effector CD8 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 329051
!Sample_description = total_rna_yield (ng): 131.496
!Sample_description = G4YW_CD8_TE
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035150
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399281
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859507
!Sample_title = G4YW_MAIT_rep3
!Sample_geo_accession = GSM2859507
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = MAIT cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: MAIT cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 300000
!Sample_description = total_rna_yield (ng): 206.772
!Sample_description = G4YW_MAIT
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035149
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399282
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859508
!Sample_title = G4YW_VD2+_rep3
!Sample_geo_accession = GSM2859508
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Vd2 gd T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Vd2 gd T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 399400
!Sample_description = total_rna_yield (ng): 304.332
!Sample_description = G4YW_VD2+
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035148
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399283
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859509
!Sample_title = G4YW_VD2-_rep3
!Sample_geo_accession = GSM2859509
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Non-Vd2 gd T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Non-Vd2 gd T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 300939
!Sample_description = total_rna_yield (ng): 139.332
!Sample_description = G4YW_VD2-
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035147
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399284
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859510
!Sample_title = G4YW_TFH_rep3
!Sample_geo_accession = GSM2859510
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Follicular helper T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Follicular helper T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 648648
!Sample_description = total_rna_yield (ng): 416.76
!Sample_description = G4YW_TFH
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035146
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399285
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859511
!Sample_title = G4YW_Treg_rep3
!Sample_geo_accession = GSM2859511
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = T regulatory cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: T regulatory cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 450000
!Sample_description = total_rna_yield (ng): 168.6
!Sample_description = G4YW_Treg
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035145
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399286
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859512
!Sample_title = G4YW_Th1_rep3
!Sample_geo_accession = GSM2859512
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Th1 cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Th1 cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 450000
!Sample_description = total_rna_yield (ng): 166.104
!Sample_description = G4YW_Th1
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035144
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399287
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859513
!Sample_title = G4YW_Th1/Th17_rep3
!Sample_geo_accession = GSM2859513
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Th1/Th17 cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Th1/Th17 cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 431351
!Sample_description = total_rna_yield (ng): 175.272
!Sample_description = G4YW_Th1/Th17
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035143
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399288
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859514
!Sample_title = G4YW_Th17_rep3
!Sample_geo_accession = GSM2859514
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Th17 cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Th17 cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 450000
!Sample_description = total_rna_yield (ng): 194.268
!Sample_description = G4YW_Th17
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035142
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399289
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859515
!Sample_title = G4YW_Th2_rep3
!Sample_geo_accession = GSM2859515
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Th2 cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Th2 cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 366973
!Sample_description = total_rna_yield (ng): 120.072
!Sample_description = G4YW_Th2
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035141
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399290
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859516
!Sample_title = G4YW_CD4_naive_rep3
!Sample_geo_accession = GSM2859516
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Naive CD4 T cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Naive CD4 T cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 450000
!Sample_description = total_rna_yield (ng): 150.12
!Sample_description = G4YW_CD4_naive
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035140
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399291
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859517
!Sample_title = G4YW_Progenitor_rep3
!Sample_geo_accession = GSM2859517
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Progenitor cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Progenitor cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 24676
!Sample_description = total_rna_yield (ng): 4.296
!Sample_description = G4YW_Progenitor
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035139
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399292
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859518
!Sample_title = G4YW_B_naive_rep3
!Sample_geo_accession = GSM2859518
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Naive B cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Naive B cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 1240800
!Sample_description = total_rna_yield (ng): 619.272
!Sample_description = G4YW_B_naive
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035264
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399293
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859519
!Sample_title = G4YW_B_NSM_rep3
!Sample_geo_accession = GSM2859519
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Non-switched memory B cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Non-switched memory B cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 275047
!Sample_description = total_rna_yield (ng): 90.984
!Sample_description = G4YW_B_NSM
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035263
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399294
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859520
!Sample_title = G4YW_B_Ex_rep3
!Sample_geo_accession = GSM2859520
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Exhausted B cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Exhausted B cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 124143
!Sample_description = total_rna_yield (ng): 44.496
!Sample_description = G4YW_B_Ex
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035257
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399295
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859521
!Sample_title = G4YW_B_SM_rep3
!Sample_geo_accession = GSM2859521
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Switched memory B cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Switched memory B cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 675060
!Sample_description = total_rna_yield (ng): 670.464
!Sample_description = G4YW_B_SM
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035262
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399296
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859522
!Sample_title = G4YW_Plasmablasts_rep3
!Sample_geo_accession = GSM2859522
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Plasmablasts
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Plasmablasts
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 93153
!Sample_description = total_rna_yield (ng): 107.928
!Sample_description = G4YW_Plasmablasts
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035261
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399297
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859523
!Sample_title = G4YW_C_mono_rep3
!Sample_geo_accession = GSM2859523
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Classical monocytes
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Classical monocytes
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 300000
!Sample_description = total_rna_yield (ng): 296.136
!Sample_description = G4YW_C_mono
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035260
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399298
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859524
!Sample_title = G4YW_I_mono_rep3
!Sample_geo_accession = GSM2859524
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Intermediate monocytes
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Intermediate monocytes
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 177839
!Sample_description = total_rna_yield (ng): 141.216
!Sample_description = G4YW_I_mono
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035259
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399299
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859525
!Sample_title = G4YW_NC_mono_rep3
!Sample_geo_accession = GSM2859525
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Non classical monocytes
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Non classical monocytes
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 300203
!Sample_description = total_rna_yield (ng): 135.048
!Sample_description = G4YW_NC_mono
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035258
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399300
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859526
!Sample_title = G4YW_NK_rep3
!Sample_geo_accession = GSM2859526
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Natural killer cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Natural killer cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 300000
!Sample_description = total_rna_yield (ng): 90.936
!Sample_description = G4YW_NK
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035138
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399301
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859527
!Sample_title = G4YW_pDC_rep3
!Sample_geo_accession = GSM2859527
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Plasmacytoid dendritic cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Plasmacytoid dendritic cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 97851
!Sample_description = total_rna_yield (ng): 158.352
!Sample_description = G4YW_pDC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035228
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399302
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859528
!Sample_title = G4YW_mDC_rep3
!Sample_geo_accession = GSM2859528
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Myeloid dendritic cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Myeloid dendritic cells
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 299149
!Sample_description = total_rna_yield (ng): 462.696
!Sample_description = G4YW_mDC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035227
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399303
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859529
!Sample_title = G4YW_Neutrophils_rep3
!Sample_geo_accession = GSM2859529
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Low-density neutrophils
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Low-density neutrophils
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 273969
!Sample_description = total_rna_yield (ng): 5.448
!Sample_description = G4YW_Neutrophils
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035226
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399304
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859530
!Sample_title = G4YW_Basophils_rep3
!Sample_geo_accession = GSM2859530
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Low-density basophils
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Low-density basophils
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 158470
!Sample_description = total_rna_yield (ng): 13.464
!Sample_description = G4YW_Basophils
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035225
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399305
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859531
!Sample_title = DZQV_PBMC_rep4
!Sample_geo_accession = GSM2859531
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = PBMCs
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: PBMCs
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 2000000
!Sample_description = total_rna_yield (ng): 284.268
!Sample_description = DZQV_PBMC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035224
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399306
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859532
!Sample_title = 925L_PBMC_rep2
!Sample_geo_accession = GSM2859532
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = PBMCs
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: PBMCs
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 2000000
!Sample_description = total_rna_yield (ng): 894.9
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!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035223
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399307
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859533
!Sample_title = 9JD4_PBMC_rep1
!Sample_geo_accession = GSM2859533
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = PBMCs
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: PBMCs
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 2000000
!Sample_description = total_rna_yield (ng): 744.096
!Sample_description = 9JD4_PBMC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035222
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399308
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859534
!Sample_title = G4YW_PBMC_rep3
!Sample_geo_accession = GSM2859534
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = PBMCs
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: PBMCs
!Sample_characteristics_ch1 = disease status: healthy
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!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 2000000
!Sample_description = total_rna_yield (ng): 842.916
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!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035221
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399309
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859535
!Sample_title = 4DUY_PBMC_rep11
!Sample_geo_accession = GSM2859535
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = PBMCs
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: PBMCs
!Sample_characteristics_ch1 = disease status: healthy
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!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 2000000
!Sample_description = total_rna_yield (ng): 961.884
!Sample_description = 4DUY_PBMC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035220
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399310
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859536
!Sample_title = 36TS_PBMC_rep12
!Sample_geo_accession = GSM2859536
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = PBMCs
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: PBMCs
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: M
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 1000000
!Sample_description = total_rna_yield (ng): 514.356
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!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035219
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399311
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0
^SAMPLE = GSM2859537
!Sample_title = CR3L_PBMC_rep13
!Sample_geo_accession = GSM2859537
!Sample_status = Public on Feb 06 2019
!Sample_submission_date = Nov 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = PBMCs
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: PBMCs
!Sample_characteristics_ch1 = disease status: healthy
!Sample_characteristics_ch1 = gender: F
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. The RNA concentration was determined using the Quant-iTTM RiboGreen® RNA Assay Kit
!Sample_extract_protocol_ch1 = The cDNA libraries were prepared from 2 ng of total RNA and 1 μl of a 1:50,000 dilution of external RNA control consortium (ERCC) spike-in control mix (Thermo Fisher Scientific) using SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1) use of 20µM template-switching oligos (TSO), 2) use of 250 pg of cDNA with 1/5 reaction mixtures of Illumina Nextera XT kit.
!Sample_description = cell_number (facs): 5000000
!Sample_description = total_rna_yield (ng): 2628.48
!Sample_description = CR3L_PBMC
!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the transcriptome with kallisto
!Sample_data_processing = Transcirpt per million (TPM) values of all trancripts were obtained with kallisto. Expression counts at gene level were obtained by summarizing transcript expression values.
!Sample_data_processing = Genome_build: GENCODE 26
!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
!Sample_platform_id = GPL11154
!Sample_contact_name = Gianni,,Monaco
!Sample_contact_email = mongianni1@gmail.com
!Sample_contact_department = Institute of Neuropathology
!Sample_contact_institute = Freiburg Medical Center
!Sample_contact_address = Breisacher Straße 64
!Sample_contact_city = Freiburg
!Sample_contact_zip/postal_code = 79106
!Sample_contact_country = Germany
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08035218
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3399312
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE107011
!Sample_series_id = GSE107019
!Sample_data_row_count = 0