^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 = GSE128027
!Series_title = Human Eosinophils Express a Distinct Gene Expression Program in Response to IL-3 Compared to Common Beta-Chain Cytokines IL-5 and GM-CSF
!Series_geo_accession = GSE128027
!Series_status = Public on Sep 06 2019
!Series_submission_date = Mar 07 2019
!Series_last_update_date = Apr 10 2020
!Series_pubmed_id = 31175163
!Series_summary = Background: Despite recent advances in asthma management with anti-IL-5 therapies, many patients with eosinophilic asthma remain poorly controlled. IL-3 shares a common beta subunit receptor with both IL-5 and GM-CSF, but through alpha subunit-specific properties, uniquely influences eosinophil biology and may serve as a potential therapeutic target.
!Series_summary = 
!Series_summary = Objective: We aimed to globally characterize the transcriptomic profiles of GM-CSF, IL-3, and IL-5 stimulation and identify differences in gene expression using advanced statistical modeling.
!Series_summary = 
!Series_summary = Methods: Human eosinophils were isolated from the peripheral blood of healthy volunteers and stimulated with either GM-CSF, IL-3 or IL-5 for 48 hours. RNA was then extracted and bulk sequencing performed. DESeq analysis identified differentially expressed genes and weighted gene co-expression network analysis independently defined modules of genes that are highly co-expressed.
!Series_summary = 
!Series_summary = Results: IL-3 stimulation yielded the most numbers of differentially expressed genes that were also highly co-expressed. GM-CSF and IL-5 stimulation demonstrated redundancy in eosinophil gene expression.
!Series_summary = 
!Series_summary = Conclusion: IL-3 produces a distinct eosinophil gene expression program among the beta-chain receptor cytokines.
!Series_overall_design = A total of 28 samples were analyzed (7 eosinophil donors, with each eosinophil collection split and independently subjected to 4 conditions - unstimulated, GM-CSF stimulated, IL-3 stimulated, IL-5 stimuated). RNA-Seq data was mapped against the hg38 reference using TopHat [15] (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Browser site.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Ryan,K,Nelson
!Series_contributor = Howard,,Brickner
!Series_contributor = Bharat,,Panwar
!Series_contributor = Ciro,,Ramirez-Suastegui
!Series_contributor = Laura,C,Alexander
!Series_contributor = Pandurangan,,Vijayanand
!Series_contributor = Grégory,,Seumois
!Series_contributor = Praveen,,Akuthota
!Series_sample_id = GSM3660549
!Series_sample_id = GSM3660550
!Series_sample_id = GSM3660551
!Series_sample_id = GSM3660552
!Series_sample_id = GSM3660553
!Series_sample_id = GSM3660554
!Series_sample_id = GSM3660555
!Series_sample_id = GSM3660556
!Series_sample_id = GSM3660557
!Series_sample_id = GSM3660558
!Series_sample_id = GSM3660559
!Series_sample_id = GSM3660560
!Series_sample_id = GSM3660561
!Series_sample_id = GSM3660562
!Series_sample_id = GSM3660563
!Series_sample_id = GSM3660564
!Series_sample_id = GSM3660565
!Series_sample_id = GSM3660566
!Series_sample_id = GSM3660567
!Series_sample_id = GSM3660568
!Series_sample_id = GSM3660569
!Series_sample_id = GSM3660570
!Series_sample_id = GSM3660571
!Series_sample_id = GSM3660572
!Series_sample_id = GSM3660573
!Series_sample_id = GSM3660574
!Series_sample_id = GSM3660575
!Series_sample_id = GSM3660576
!Series_contact_name = Pandurangan,,Vijayanand
!Series_contact_email = vijay@lji.org
!Series_contact_laboratory = Vijayanand Lab
!Series_contact_department = Vaccine Discovery
!Series_contact_institute = La Jolla Institute for Immunology
!Series_contact_address = 9420 Athena Circle
!Series_contact_city = San Diego
!Series_contact_state = California
!Series_contact_zip/postal_code = 92037
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128027/suppl/GSE128027_Nelson_TPM.txt.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128027/suppl/GSE128027_Nelson_raw_counts.txt.gz
!Series_platform_id = GPL16791
!Series_platform_taxid = 9606
!Series_sample_taxid = 9606
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA526069
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP187898
^PLATFORM = GPL16791
!Platform_title = Illumina HiSeq 2500 (Homo sapiens)
!Platform_geo_accession = GPL16791
!Platform_status = Public on Mar 14 2013
!Platform_submission_date = Mar 14 2013
!Platform_last_update_date = Mar 27 2019
!Platform_technology = high-throughput sequencing
!Platform_distribution = virtual
!Platform_organism = Homo sapiens
!Platform_taxid = 9606
!Platform_contact_name = ,,GEO
!Platform_contact_country = USA
!Platform_data_row_count = 0
^SAMPLE = GSM3660549
!Sample_title = GMCSF_005
!Sample_geo_accession = GSM3660549
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D5
!Sample_characteristics_ch1 = stimulation: GMCSF
!Sample_characteristics_ch1 = run_id: 4633
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086294
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493913
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660550
!Sample_title = GMCSF_008
!Sample_geo_accession = GSM3660550
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D8
!Sample_characteristics_ch1 = stimulation: GMCSF
!Sample_characteristics_ch1 = run_id: 4633
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086293
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493914
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660551
!Sample_title = IL3_005
!Sample_geo_accession = GSM3660551
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D5
!Sample_characteristics_ch1 = stimulation: IL3
!Sample_characteristics_ch1 = run_id: 4633
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086292
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493915
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660552
!Sample_title = IL3_008
!Sample_geo_accession = GSM3660552
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D8
!Sample_characteristics_ch1 = stimulation: IL3
!Sample_characteristics_ch1 = run_id: 4633
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086291
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493916
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660553
!Sample_title = IL5_005
!Sample_geo_accession = GSM3660553
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D5
!Sample_characteristics_ch1 = stimulation: IL5
!Sample_characteristics_ch1 = run_id: 4633
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086290
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493917
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660554
!Sample_title = IL5_008
!Sample_geo_accession = GSM3660554
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D8
!Sample_characteristics_ch1 = stimulation: IL5
!Sample_characteristics_ch1 = run_id: 4633
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086289
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493918
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660555
!Sample_title = neg_control_005
!Sample_geo_accession = GSM3660555
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D5
!Sample_characteristics_ch1 = stimulation: NegCtrl
!Sample_characteristics_ch1 = run_id: 4633
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086288
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493919
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660556
!Sample_title = neg_control_008
!Sample_geo_accession = GSM3660556
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D8
!Sample_characteristics_ch1 = stimulation: NegCtrl
!Sample_characteristics_ch1 = run_id: 4633
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086287
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493920
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660557
!Sample_title = 09_007_NegCtrl
!Sample_geo_accession = GSM3660557
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D7
!Sample_characteristics_ch1 = stimulation: NegCtrl
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086286
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493921
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660558
!Sample_title = 10_007_IL3
!Sample_geo_accession = GSM3660558
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D7
!Sample_characteristics_ch1 = stimulation: IL3
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086285
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493922
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660559
!Sample_title = 11_007_IL5
!Sample_geo_accession = GSM3660559
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D7
!Sample_characteristics_ch1 = stimulation: IL5
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086284
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493923
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660560
!Sample_title = 12_007_GMCSF
!Sample_geo_accession = GSM3660560
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D7
!Sample_characteristics_ch1 = stimulation: GMCSF
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086283
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493924
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660561
!Sample_title = 13_006_NegCtrl
!Sample_geo_accession = GSM3660561
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D6
!Sample_characteristics_ch1 = stimulation: NegCtrl
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086281
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493925
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660562
!Sample_title = 14_006_IL3
!Sample_geo_accession = GSM3660562
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D6
!Sample_characteristics_ch1 = stimulation: IL3
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086280
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493926
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660563
!Sample_title = 15_006_IL5
!Sample_geo_accession = GSM3660563
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D6
!Sample_characteristics_ch1 = stimulation: IL5
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086278
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493927
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660564
!Sample_title = 16_006_GMCSF
!Sample_geo_accession = GSM3660564
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D6
!Sample_characteristics_ch1 = stimulation: GMCSF
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086276
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493928
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660565
!Sample_title = 17_002_NegCtrl
!Sample_geo_accession = GSM3660565
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D2
!Sample_characteristics_ch1 = stimulation: NegCtrl
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086275
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493929
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660566
!Sample_title = 18_002_IL3
!Sample_geo_accession = GSM3660566
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D2
!Sample_characteristics_ch1 = stimulation: IL3
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086273
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493930
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660567
!Sample_title = 19_002_IL5
!Sample_geo_accession = GSM3660567
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D2
!Sample_characteristics_ch1 = stimulation: IL5
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086272
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493931
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660568
!Sample_title = 20_002_GMCSF
!Sample_geo_accession = GSM3660568
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D2
!Sample_characteristics_ch1 = stimulation: GMCSF
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086270
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493932
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660569
!Sample_title = 21_018_NegCtrl
!Sample_geo_accession = GSM3660569
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D18
!Sample_characteristics_ch1 = stimulation: NegCtrl
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086268
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493933
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660570
!Sample_title = 22_018_IL3
!Sample_geo_accession = GSM3660570
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D18
!Sample_characteristics_ch1 = stimulation: IL3
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086305
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493934
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660571
!Sample_title = 23_018_IL5
!Sample_geo_accession = GSM3660571
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D18
!Sample_characteristics_ch1 = stimulation: IL5
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086303
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493935
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660572
!Sample_title = 24_018_GMCSF
!Sample_geo_accession = GSM3660572
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D18
!Sample_characteristics_ch1 = stimulation: GMCSF
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086301
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493936
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660573
!Sample_title = 25_019_NegCtrl
!Sample_geo_accession = GSM3660573
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D19
!Sample_characteristics_ch1 = stimulation: NegCtrl
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086300
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493937
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660574
!Sample_title = 26_019_IL3
!Sample_geo_accession = GSM3660574
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D19
!Sample_characteristics_ch1 = stimulation: IL3
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086298
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493938
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660575
!Sample_title = 27_019_IL5
!Sample_geo_accession = GSM3660575
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D19
!Sample_characteristics_ch1 = stimulation: IL5
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086297
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493939
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0
^SAMPLE = GSM3660576
!Sample_title = 28_019_GMCSF
!Sample_geo_accession = GSM3660576
!Sample_status = Public on Sep 06 2019
!Sample_submission_date = Mar 07 2019
!Sample_last_update_date = Sep 06 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Venous blood
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Venous blood
!Sample_characteristics_ch1 = cell type: Eosinophils
!Sample_characteristics_ch1 = donor_id: D19
!Sample_characteristics_ch1 = stimulation: GMCSF
!Sample_characteristics_ch1 = run_id: 4692
!Sample_treatment_protocol_ch1 = Recombinant IL-3, IL-5 (R&D Systems, Minneapolis, MN) and GM-CSF (BioLegend, San Diego, CA) were used for chemokine stimulation, all for 48 hours at a concentration of 10 ng/ml in RPMI-1640 at 37 o C. We also kept an unstimulated fraction.
!Sample_growth_protocol_ch1 = No particular cell groth procedure was required. Whole blood (160 ml) was drawn from healthy volunteers without known allergic disease. Red blood cells (RBCs) were depleted by hetastarch incubation followed by gravity separation. Granulocytes were isolated by centrifugation of RBC-depleted blood over a Ficoll gradient. Eosinophils were then isolated from the granulocyte fraction by incubation with a cocktail of negative selection antibodies followed by passage over a magnetized column.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Total RNA was isolated using miRNeasy micro kit (Qiagen) loaded on an automated platform (Qiacube, Qiagen) and quantified as described previously (Seumois et al.Am J Clin Exp Immunol. 2012; PMID:23304658).
!Sample_extract_protocol_ch1 = Barcoded Illumina sequencing libraries (Nextera; Illumina) were generated utilizing an automated platform (Biomek FXP, Beckman Coulter). RNA-Seq - Sequencing platform, HiSeq2500 (Illumina). Libraries were sequenced to obtain more than 8 million 50-bp single-end reads (HiSeq Rapid Run Cluster and SBS Kit V2; Illumina).
!Sample_description = Purified cells by negative selection (StemCell Technologies, Vancouver, Canada)
!Sample_description = Nelson_raw_counts.txt
!Sample_description = Nelson_TPM.txt
!Sample_data_processing = RNA-Seq data was mapped against the hg38 reference using TopHat (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Bioinformatics site
!Sample_data_processing = Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -texon -i gene_id,http://www-huber.embl.de/users/anders/HTSeq). Counts per gene are obtained by counting all the transcripts mapping to a gene and is together referred to as transcript.
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_TPM.txt.gz contains Transcript per Million normalized counts
!Sample_data_processing = Supplementary_files_format_and_content: Nelson_raw_counts.txt.gz contains raw counts of sequencing reads obtained with HTSeq-count
!Sample_platform_id = GPL16791
!Sample_contact_name = Pandurangan,,Vijayanand
!Sample_contact_email = vijay@lji.org
!Sample_contact_laboratory = Vijayanand Lab
!Sample_contact_department = Vaccine Discovery
!Sample_contact_institute = La Jolla Institute for Immunology
!Sample_contact_address = 9420 Athena Circle
!Sample_contact_city = San Diego
!Sample_contact_state = California
!Sample_contact_zip/postal_code = 92037
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11086296
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5493940
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE128027
!Sample_data_row_count = 0