GSE92904 Genetic analysis of isoform usage in the human anti-viral response

Contributors : Chun J Ye ; Jenny Chen ; Alexandra-Chlo é Villani ; Meena Subramaniam ; Rachel E Gate ; Tushar Bhangale ; Mark N Lee ; Towfique Raj ; Raktima Raychowdhury ; Weibo Li ; Noga Rogel ; Sean Simmons ; Selina H Imboywa ; Portia I Chipendo ; Cristin McCabe ; Michelle H Lee ; Irene Y Frohlich ; Barbara E Stranger ; Philip L De Jager ; A viv Regev ; Tim Behrens ; Nir HacohenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWhile genetic variants are known to be associated with overall gene abundance in stimulated immune cells, less is known about their effects on alternative isoform usage. Analyzing RNA-seq profiles of monocyte-derived dendritic cells from 243 individuals, we uncovered thousands of unannotated isoforms synthesized in response to influenza infection and type 1 interferon stimulation. We identified more than a thousand quantitative trait loci (QTLs) associated with alternate isoform usage (isoQTLs), many of which are independent of expression QTLs for the same gene. Compared to eQTLs, isoQTLs are enriched for splice sites and untranslated regions, but depleted of sequences upstream of annotated transcription start sites. Both eQTLs and isoQTLs explain a significant proportion of the disease heritability attributed to common genetic variants.

Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research