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Series GSE87290 Query DataSets for GSE87290
Status Public on Sep 27, 2016
Title RNA-seq of human peripheral blood mononuclear cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Inflammatory cytokine responses to activation of innate immunity differ between individuals, yet the genomic and transcriptomic determinants of inflammatory responsiveness are not well understood. We hypothesized that mRNA and lincRNA expression is modulated in disease-relevant tissues in humans in vivo during inflammation, and differs between individuals with divergent evoked inflammatory responses. In the Genetics of Evoked Response to Niacin and Endotoxemia (GENE) Study, we performed an inpatient endotoxin challenge (1ng/kg LPS) in healthy humans. We selected individuals in the top (high-responders) and bottom (low-responders) extremes for inflammatory responses, and applied RNASeq to peripheral blood mononuclear cells (PBMC, n=15) before and after LPS administration. At baseline, there were limited differences in gene expression by sex or race. Further, only a small number of genes differed between high and low responders at baseline. Post-LPS, there were clear differences in the magnitude of the transcriptional response between high and low responders, with a far greater number of genes differentially expressed post-LPS in high responders, consistent with the clinical response. We also found a number of differentially expressed long intergenic non-coding RNAs (lincRNAs) post-LPS. We show that differences in gene expression may drive differences in clinical inflammatory response, and that differentially expressed genes and lincRNAs represent novel candidates for modulation of immune and metabolic responses in acute and chronic diseases.
Overall design Peripheral blood mononuclear cells (PBMCs) from 15 healthy subjects were sequenced by Illumina HiSeq 2000 with poly-A selection
Contributor(s) Ferguson J, Xue C
Citation(s) 27230130
Submission date Sep 22, 2016
Last update date May 15, 2019
Contact name Chenyi Xue
Organization name Columbia University
Street address 630 W 168th St.
City New York
State/province NY
ZIP/Postal code 10032
Country USA
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (30)
GSM2326887 PBMC_replicate_1 baseline high inflammation
GSM2326888 PBMC_replicate_2 baseline high inflammation
GSM2326889 PBMC_replicate_3 baseline high inflammation
BioProject PRJNA343985
SRA SRP090337

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Supplementary file Size Download File type/resource
GSE87290_PBMC_high_pre_vs_post_gene_exp.diff.gz 1.1 Mb (ftp)(http) DIFF
GSE87290_PBMC_low_pre_vs_post_gene_exp.diff.gz 1.0 Mb (ftp)(http) DIFF
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