^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 = GSE139358
!Series_title = Transcriptomic, epigenetic and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus [RNA-seq]
!Series_geo_accession = GSE139358
!Series_status = Public on Nov 22 2019
!Series_submission_date = Oct 24 2019
!Series_last_update_date = Nov 25 2019
!Series_pubmed_id = 31754025
!Series_summary = Two subpopulations of low density granulocytes (LDGs) were defined in terms of different gene expression patterns, transcriptional and epigenetic features as well as functions. This study provides insights into the mechanism of immune dysregulation and the vascular damage characteristic of lupus.
!Series_overall_design = Transcriptomics and epigenetic assessment of lupus PBMCs, LDGs, autologous normal-density neutrophils (NDN) and healthy control (HC) neutrophils was performed by mRNA sequencing and assay for transposase-accessible chromatin sequencing. NET formation, chemotaxis, phagocytosis, degranulation, induction of endothelial dysfunction and release of oxidized nucleic acids were compared among subsets. This metadata sheet includes 51 RNA-Seq samples of this project.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = P,,Mistry
!Series_contributor = S,,Nakabo
!Series_contributor = L,,O’Neil
!Series_contributor = R,R,Goel
!Series_contributor = K,,Jiang
!Series_contributor = S,,Gupta
!Series_contributor = S,,Dell’Orso
!Series_contributor = G,,Gutierrez-Cruz
!Series_contributor = H,W,Sun
!Series_contributor = M,J,Kaplan
!Series_sample_id = GSM4138684
!Series_sample_id = GSM4138685
!Series_sample_id = GSM4138686
!Series_sample_id = GSM4138687
!Series_sample_id = GSM4138688
!Series_sample_id = GSM4138689
!Series_sample_id = GSM4138690
!Series_sample_id = GSM4138691
!Series_sample_id = GSM4138692
!Series_sample_id = GSM4138693
!Series_sample_id = GSM4138694
!Series_sample_id = GSM4138695
!Series_sample_id = GSM4138696
!Series_sample_id = GSM4138697
!Series_sample_id = GSM4138698
!Series_sample_id = GSM4138699
!Series_sample_id = GSM4138700
!Series_sample_id = GSM4138701
!Series_sample_id = GSM4138702
!Series_sample_id = GSM4138703
!Series_sample_id = GSM4138704
!Series_sample_id = GSM4138705
!Series_sample_id = GSM4138706
!Series_sample_id = GSM4138707
!Series_sample_id = GSM4138708
!Series_sample_id = GSM4138709
!Series_sample_id = GSM4138710
!Series_sample_id = GSM4138711
!Series_sample_id = GSM4138712
!Series_sample_id = GSM4138713
!Series_sample_id = GSM4138714
!Series_sample_id = GSM4138715
!Series_sample_id = GSM4138716
!Series_sample_id = GSM4138717
!Series_sample_id = GSM4138718
!Series_sample_id = GSM4138719
!Series_sample_id = GSM4138720
!Series_sample_id = GSM4138721
!Series_sample_id = GSM4138722
!Series_sample_id = GSM4138723
!Series_sample_id = GSM4138724
!Series_sample_id = GSM4138725
!Series_sample_id = GSM4138726
!Series_sample_id = GSM4138727
!Series_sample_id = GSM4138728
!Series_sample_id = GSM4138729
!Series_sample_id = GSM4138730
!Series_sample_id = GSM4138731
!Series_sample_id = GSM4138732
!Series_sample_id = GSM4138733
!Series_sample_id = GSM4138734
!Series_contact_name = Hong-wei,,Sun
!Series_contact_laboratory = Biodata Mining & Discovery Section
!Series_contact_department = Office of Science & Technology
!Series_contact_institute = NIAMS
!Series_contact_address = 9000 Rockville Pile
!Series_contact_city = Bethesda
!Series_contact_state = MD
!Series_contact_zip/postal_code = 20892
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE139nnn/GSE139358/suppl/GSE139358_RNA-Seq_gene_rpkm_18_samples.xlsx
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE139nnn/GSE139358/suppl/GSE139358_RNA-Seq_gene_rpkm_33_samples.xlsx
!Series_platform_id = GPL21290
!Series_platform_taxid = 9606
!Series_sample_taxid = 9606
!Series_relation = SubSeries of: GSE139360
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA579374
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP226877
^PLATFORM = GPL21290
!Platform_title = Illumina HiSeq 3000 (Homo sapiens)
!Platform_geo_accession = GPL21290
!Platform_status = Public on Dec 31 2015
!Platform_submission_date = Dec 31 2015
!Platform_last_update_date = Dec 23 2018
!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 = GSM4138684
!Sample_title = NDN_ctrl_01 [RNA-seq]
!Sample_geo_accession = GSM4138684
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Healthy (control)
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R01
!Sample_description = Exp ID: 170208_0025_s01
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109286
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052811
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138685
!Sample_title = NDN_ctrl_02 [RNA-seq]
!Sample_geo_accession = GSM4138685
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Healthy (control)
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R02
!Sample_description = Exp ID: 161229_0016_s02
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109285
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052812
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138686
!Sample_title = NDN_ctrl_03 [RNA-seq]
!Sample_geo_accession = GSM4138686
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Healthy (control)
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R03
!Sample_description = Exp ID: 161229_0016_s07
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109320
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052813
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138687
!Sample_title = NDN_ctrl_04 [RNA-seq]
!Sample_geo_accession = GSM4138687
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Healthy (control)
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R04
!Sample_description = Exp ID: 161229_0016_s08
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109319
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052814
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138688
!Sample_title = NDN_ctrl_05 [RNA-seq]
!Sample_geo_accession = GSM4138688
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Healthy (control)
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R05
!Sample_description = Exp ID: 170208_0025_s09
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109318
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052815
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138689
!Sample_title = NDN_ctrl_06 [RNA-seq]
!Sample_geo_accession = GSM4138689
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Healthy (control)
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R06
!Sample_description = Exp ID: 170208_0025_s11
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109317
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052816
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138690
!Sample_title = NDN_ctrl_07 [RNA-seq]
!Sample_geo_accession = GSM4138690
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Healthy (control)
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R07
!Sample_description = Exp ID: 161229_0016_s12
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109316
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052817
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138691
!Sample_title = NDN_ctrl_08 [RNA-seq]
!Sample_geo_accession = GSM4138691
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Healthy (control)
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R08
!Sample_description = Exp ID: 161229_0016_s15
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109315
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052818
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138692
!Sample_title = NDN_ctrl_09 [RNA-seq]
!Sample_geo_accession = GSM4138692
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Healthy (control)
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R09
!Sample_description = Exp ID: 161229_0016_s16
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109314
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052819
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138693
!Sample_title = NDN_ctrl_10 [RNA-seq]
!Sample_geo_accession = GSM4138693
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Healthy (control)
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R10
!Sample_description = Exp ID: 161229_0016_s20
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109313
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052820
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138694
!Sample_title = NDN_ctrl_11 [RNA-seq]
!Sample_geo_accession = GSM4138694
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Healthy (control)
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R11
!Sample_description = Exp ID: 161229_0016_s21
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109312
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052821
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138695
!Sample_title = NDN_SLE_01 [RNA-seq]
!Sample_geo_accession = GSM4138695
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
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!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R12
!Sample_description = Exp ID: 161229_0016_s01
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109311
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052822
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138696
!Sample_title = NDN_SLE_02 [RNA-seq]
!Sample_geo_accession = GSM4138696
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
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!Sample_taxid_ch1 = 9606
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!Sample_molecule_ch1 = total RNA
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!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R13
!Sample_description = Exp ID: 170208_0025_s03
!Sample_description = mRNA
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!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109310
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052823
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138697
!Sample_title = NDN_SLE_03 [RNA-seq]
!Sample_geo_accession = GSM4138697
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
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!Sample_molecule_ch1 = total RNA
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!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R14
!Sample_description = Exp ID: 161229_0016_s04
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109309
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052824
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138698
!Sample_title = NDN_SLE_04 [RNA-seq]
!Sample_geo_accession = GSM4138698
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
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!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
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!Sample_molecule_ch1 = total RNA
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!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R15
!Sample_description = Exp ID: 170208_0025_s07
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109308
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052825
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138699
!Sample_title = NDN_SLE_05 [RNA-seq]
!Sample_geo_accession = GSM4138699
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
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!Sample_taxid_ch1 = 9606
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!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R16
!Sample_description = Exp ID: 161229_0016_s09
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109307
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052826
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138700
!Sample_title = NDN_SLE_06 [RNA-seq]
!Sample_geo_accession = GSM4138700
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R17
!Sample_description = Exp ID: 161229_0016_s10
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109306
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052827
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138701
!Sample_title = NDN_SLE_07 [RNA-seq]
!Sample_geo_accession = GSM4138701
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R18
!Sample_description = Exp ID: 161229_0016_s13
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109305
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052828
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138702
!Sample_title = NDN_SLE_08 [RNA-seq]
!Sample_geo_accession = GSM4138702
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R19
!Sample_description = Exp ID: 161229_0016_s17
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109304
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052829
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138703
!Sample_title = NDN_SLE_09 [RNA-seq]
!Sample_geo_accession = GSM4138703
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R20
!Sample_description = Exp ID: 161229_0016_s22
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109303
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052830
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138704
!Sample_title = NDN_SLE_10 [RNA-seq]
!Sample_geo_accession = GSM4138704
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R21
!Sample_description = Exp ID: 161229_0016_s23
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109302
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052831
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138705
!Sample_title = NDN_SLE_11 [RNA-seq]
!Sample_geo_accession = GSM4138705
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R22
!Sample_description = Exp ID: 161229_0016_s26
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109301
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052832
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138706
!Sample_title = LDG_SLE_01_mat [RNA-seq]
!Sample_geo_accession = GSM4138706
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: LDG
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R23
!Sample_description = Exp ID: 161229_0016_s03
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109300
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052833
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138707
!Sample_title = LDG_SLE_02_imm [RNA-seq]
!Sample_geo_accession = GSM4138707
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: LDG
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R24
!Sample_description = Exp ID: 161229_0016_s05
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109344
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052834
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138708
!Sample_title = LDG_SLE_03_mat [RNA-seq]
!Sample_geo_accession = GSM4138708
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: LDG
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R25
!Sample_description = Exp ID: 170208_0025_s05
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109343
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052835
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138709
!Sample_title = LDG_SLE_04_mat [RNA-seq]
!Sample_geo_accession = GSM4138709
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: LDG
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R26
!Sample_description = Exp ID: 161229_0016_s06
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109342
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052836
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138710
!Sample_title = LDG_SLE_05_mat [RNA-seq]
!Sample_geo_accession = GSM4138710
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: LDG
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R27
!Sample_description = Exp ID: 161229_0016_s11
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109341
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052837
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138711
!Sample_title = LDG_SLE_06_imm [RNA-seq]
!Sample_geo_accession = GSM4138711
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: LDG
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R28
!Sample_description = Exp ID: 161229_0016_s14
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109340
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052838
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138712
!Sample_title = LDG_SLE_07_imm [RNA-seq]
!Sample_geo_accession = GSM4138712
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: LDG
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R29
!Sample_description = Exp ID: 161229_0016_s18
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109339
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052839
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138713
!Sample_title = LDG_SLE_08_mat [RNA-seq]
!Sample_geo_accession = GSM4138713
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: LDG
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R30
!Sample_description = Exp ID: 161229_0016_s19
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
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!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109338
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052840
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138714
!Sample_title = LDG_SLE_09_mat [RNA-seq]
!Sample_geo_accession = GSM4138714
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
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!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
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!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R31
!Sample_description = Exp ID: 161229_0016_s24
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
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!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109337
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052841
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138715
!Sample_title = LDG_SLE_10_mat [RNA-seq]
!Sample_geo_accession = GSM4138715
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
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!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R32
!Sample_description = Exp ID: 161229_0016_s25
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
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!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109336
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052842
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138716
!Sample_title = LDG_SLE_11_mat [RNA-seq]
!Sample_geo_accession = GSM4138716
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
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!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
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!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R33
!Sample_description = Exp ID: 161229_0016_s27
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_33_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109335
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052843
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138717
!Sample_title = NDN_01_LE [RNA-seq]
!Sample_geo_accession = GSM4138717
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
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!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
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!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R34
!Sample_description = Exp ID: 180611_0143_s01
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109334
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052844
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138718
!Sample_title = NDN_02_LE [RNA-seq]
!Sample_geo_accession = GSM4138718
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: NDN
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R35
!Sample_description = Exp ID: 180611_0143_s02
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109333
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052845
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138719
!Sample_title = NDN_03_LE [RNA-seq]
!Sample_geo_accession = GSM4138719
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
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!Sample_molecule_ch1 = total RNA
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!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R36
!Sample_description = Exp ID: 180611_0143_s06
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
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!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109332
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052846
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138720
!Sample_title = NDN_04_PPAR [RNA-seq]
!Sample_geo_accession = GSM4138720
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
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!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R37
!Sample_description = Exp ID: 180611_0143_s03
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!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
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!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
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!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109331
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052847
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138721
!Sample_title = NDN_05_PPAR [RNA-seq]
!Sample_geo_accession = GSM4138721
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
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!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R38
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!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
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!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
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!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
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!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109330
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052848
!Sample_supplementary_file_1 = NONE
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!Sample_series_id = GSE139360
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^SAMPLE = GSM4138722
!Sample_title = NDN_06_PPAR [RNA-seq]
!Sample_geo_accession = GSM4138722
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
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!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
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!Sample_description = mRNA
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!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
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!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
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!Sample_instrument_model = Illumina HiSeq 3000
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052849
!Sample_supplementary_file_1 = NONE
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^SAMPLE = GSM4138723
!Sample_title = LDG_01_LE_CD10_pos [RNA-seq]
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!Sample_last_update_date = Nov 22 2019
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!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
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!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052850
!Sample_supplementary_file_1 = NONE
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^SAMPLE = GSM4138724
!Sample_title = LDG_02_LE_CD10_pos [RNA-seq]
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!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
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!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
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!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
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!Sample_instrument_model = Illumina HiSeq 3000
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^SAMPLE = GSM4138725
!Sample_title = LDG_03_LE_CD10_pos [RNA-seq]
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!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
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!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
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!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
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!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
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^SAMPLE = GSM4138726
!Sample_title = LDG_04_PPAR_CD10_pos [RNA-seq]
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!Sample_last_update_date = Nov 22 2019
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!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
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!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
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!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
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^SAMPLE = GSM4138727
!Sample_title = LDG_05_PPAR_CD10_pos [RNA-seq]
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!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
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!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
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!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
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!Sample_contact_address = 9000 Rockville Pile
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!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
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!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109324
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052854
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138728
!Sample_title = LDG_06_PPAR_CD10_pos [RNA-seq]
!Sample_geo_accession = GSM4138728
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: LDG
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R45
!Sample_description = Exp ID: 180611_0143_s12
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109323
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052855
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138729
!Sample_title = LDG_01_LE_CD10_neg [RNA-seq]
!Sample_geo_accession = GSM4138729
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: LDG
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R46
!Sample_description = Exp ID: 180611_0143_s13
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109322
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052856
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138730
!Sample_title = LDG_02_LE_CD10_neg [RNA-seq]
!Sample_geo_accession = GSM4138730
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: LDG
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R47
!Sample_description = Exp ID: 180611_0143_s14
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109321
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052857
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138731
!Sample_title = LDG_03_LE_CD10_neg [RNA-seq]
!Sample_geo_accession = GSM4138731
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: LDG
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R48
!Sample_description = Exp ID: 180611_0143_s16
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109356
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052858
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138732
!Sample_title = LDG_04_PPAR_CD10_neg [RNA-seq]
!Sample_geo_accession = GSM4138732
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: LDG
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R49
!Sample_description = Exp ID: 180611_0143_s15
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109355
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052859
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138733
!Sample_title = LDG_05_PPAR_CD10_neg [RNA-seq]
!Sample_geo_accession = GSM4138733
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: LDG
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R50
!Sample_description = Exp ID: 180611_0143_s17
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109354
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052860
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0
^SAMPLE = GSM4138734
!Sample_title = LDG_06_PPAR_CD10_neg [RNA-seq]
!Sample_geo_accession = GSM4138734
!Sample_status = Public on Nov 22 2019
!Sample_submission_date = Oct 24 2019
!Sample_last_update_date = Nov 22 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Human whole blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = diagnosis: Lupus
!Sample_characteristics_ch1 = cell type: LDG
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Peripheral blood was collected by heparinized tubes and the PBMC fraction was obtained using Ficoll/Hypaque gradient. Bulk LDGs were isolated by magnetic bead negative selection. CD10+ LDGs, CD10- LDGs, and CD10+ NDN were sorted by flow cytometry using CD10-APC,CD14-FITC and CD15-PE antibodies. RNA was isolated using Zymo Research Direc-Zol RNA Miniprep kit.
!Sample_extract_protocol_ch1 = cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina).
!Sample_extract_protocol_ch1 = RNA seq data were generated on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
!Sample_description = R51
!Sample_description = Exp ID: 180611_0143_s18
!Sample_description = mRNA
!Sample_description = processed data file: RNA-Seq_gene_rpkm_18_samples.xlsx
!Sample_data_processing = Alignment: Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1.
!Sample_data_processing = RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6.
!Sample_data_processing = Genome_build: hg19 (GRCh37)
!Sample_data_processing = Supplementary_files_format_and_content: RNA-Seq_gene_rpkm_*.xlsx: Excel files for gene expression RPKM.
!Sample_platform_id = GPL21290
!Sample_contact_name = Hong-wei,,Sun
!Sample_contact_laboratory = Biodata Mining & Discovery Section
!Sample_contact_department = Office of Science & Technology
!Sample_contact_institute = NIAMS
!Sample_contact_address = 9000 Rockville Pile
!Sample_contact_city = Bethesda
!Sample_contact_state = MD
!Sample_contact_zip/postal_code = 20892
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 3000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN13109353
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX7052861
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE139358
!Sample_series_id = GSE139360
!Sample_data_row_count = 0