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GSE72502

GSE GEO
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Healthy donor PBMC RNA-seq with or without interferon-alpha stimulation

Organism: Homo sapiens
Platform: GPL9052
Samples: 6
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Aug 28 2015
Last Updated: May 15 2019
Status: Public on Sep 16 2015
Contact: Tiffany,,hung (Genentech)

Relations

SubSeries of: GSE72420 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA294173 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP062958

Summary

Determine the gene expression profile in peripheral blood monocytes isolated from 3 healthy donors +/- 6 hours of interferon-alpha treatment.

Overall Design

3 healthy donor PBMCs +/- interferon-alpha.

Analysis (5 steps)

View Data Processing
Processing steps for GSE72502
  1. Illumina software used for basecalling.
  2. Sequenced reads were trimmed for adaptor sequence, filtered for rRNA contamination, filtered for low-complexity or low-quality sequence, then mapped to hg19 whole genome using GSNAP.
  3. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
  4. In short, exons from all isoforms of a gene were merged to create one meta-transcript.
  5. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

Supplementary Files (1)

GSE72502_PBMC_RPKMs.xls.gz Download
GEO Samples (6)
GSM1863325 GSM1863326 GSM1863327 GSM1863328 GSM1863329 GSM1863330

Dataset Citations (1)

The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression.
PMID 26382853 · 2015 · Science (New York, N.Y.)
T Hung, G A Pratt, B Sundararaman, M J Townsend, C Chaivorapol, T Bhangale, R R Graham, W Ortmann, L A Criswell, G W Yeo, T W Behrens

SRA Experiments (6) and Runs (6)

Total: 17099 MB
SRX1167613 SRP062958 RNA-Seq PAIRED
GSM1863325: 1. PBMC; Homo sapiens; RNA-Seq
Sample: SRS1047512
BioProject: PRJNA294173
BioSample: SAMN04017638
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Homo sapiens
Sample attributes
source_name: human blood donor peripheral blood monocyte, untreated
disease state: healthy
cell type: peripheral blood monocytes
treatment: none
donor id: A
Original files (1)
human blood donor peripheral blood monocyte, untreated
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR2192716 23096184 3464427600 2120.48 LIB8212_SAM2707860_L1_R1.fastq.gz, LIB8212_SAM2707860_L1_R2.fastq.gz,… SRA
SRX1167614 SRP062958 RNA-Seq PAIRED
GSM1863326: 2. PBMC; Homo sapiens; RNA-Seq
Sample: SRS1047511
BioProject: PRJNA294173
BioSample: SAMN04017639
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Homo sapiens
Sample attributes
source_name: human blood donor peripheral blood monocyte, untreated
disease state: healthy
cell type: peripheral blood monocytes
treatment: none
donor id: B
Original files (1)
human blood donor peripheral blood monocyte, untreated
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR2192717 28943068 4341460200 2651.31 LIB8215_SAM2707863_L1_R1.fastq.gz, LIB8215_SAM2707863_L1_R2.fastq.gz,… SRA
SRX1167615 SRP062958 RNA-Seq PAIRED
GSM1863327: 3. PBMC; Homo sapiens; RNA-Seq
Sample: SRS1047510
BioProject: PRJNA294173
BioSample: SAMN04017640
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Homo sapiens
Sample attributes
source_name: human blood donor peripheral blood monocyte, untreated
disease state: healthy
cell type: peripheral blood monocytes
treatment: none
donor id: C
Original files (1)
human blood donor peripheral blood monocyte, untreated
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR2192718 35669846 5350476900 3279.08 LIB8209_SAM2707857_L1_R1.fastq.gz, LIB8209_SAM2707857_L1_R2.fastq.gz,… SRA
SRX1167616 SRP062958 RNA-Seq PAIRED
GSM1863328: 4. PBMC + IFNa; Homo sapiens; RNA-Seq
Sample: SRS1047509
BioProject: PRJNA294173
BioSample: SAMN04017641
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Homo sapiens
Sample attributes
source_name: human blood donor peripheral blood monocyte, IFNa
disease state: healthy
cell type: peripheral blood monocytes
treatment: interferon-alpha
donor id: B
Original files (1)
human blood donor peripheral blood monocyte, IFNa
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR2192719 54167215 8125082250 4799.93 LIB8566_SAM2707864_L5_R1.fastq.gz, LIB8566_SAM2707864_L5_R2.fastq.gz,… SRA
SRX1167617 SRP062958 RNA-Seq PAIRED
GSM1863329: 5. PBMC + IFNa; Homo sapiens; RNA-Seq
Sample: SRS1047508
BioProject: PRJNA294173
BioSample: SAMN04017642
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Homo sapiens
Sample attributes
source_name: human blood donor peripheral blood monocyte, IFNa
disease state: healthy
cell type: peripheral blood monocytes
treatment: interferon-alpha
donor id: A
Original files (1)
human blood donor peripheral blood monocyte, IFNa
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR2192720 21427378 3214106700 1955.72 LIB8213_SAM2707861_L1_R1.fastq.gz, LIB8213_SAM2707861_L1_R2.fastq.gz,… SRA
SRX1167618 SRP062958 RNA-Seq PAIRED
GSM1863330: 6. PBMC + IFNa; Homo sapiens; RNA-Seq
Sample: SRS1047507
BioProject: PRJNA294173
BioSample: SAMN04017643
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Homo sapiens
Sample attributes
source_name: human blood donor peripheral blood monocyte, IFNa
disease state: healthy
cell type: peripheral blood monocytes
treatment: interferon-alpha
donor id: C
Original files (1)
human blood donor peripheral blood monocyte, IFNa
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR2192721 25100512 3765076800 2292.6 LIB8210_SAM2707858_L1_R1.fastq.gz, LIB8210_SAM2707858_L1_R2.fastq.gz,… SRA

Linked Publications (1)

The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression.
Science (New York, N.Y.) · 2015

Data Files (6)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— LIB8209_SAM2707857_L1_R1.fastq.gz RNA-Seq 3.2 GB link
— LIB8210_SAM2707858_L1_R1.fastq.gz RNA-Seq 2.2 GB link
— LIB8212_SAM2707860_L1_R1.fastq.gz RNA-Seq 2.1 GB link
— LIB8213_SAM2707861_L1_R1.fastq.gz RNA-Seq 1.9 GB link
— LIB8215_SAM2707863_L1_R1.fastq.gz RNA-Seq 2.6 GB link
— LIB8566_SAM2707864_L5_R1.fastq.gz RNA-Seq 4.7 GB link