RNA-seq time course on human CD4 memory T cells stimulated with anti-CD3/CD28 beads

In this study we sought to analyze the effects of genetic variants on gene regulation in a cell-state dependent manner during CD4 memory T cell activation. To do this, we performed an RNA-seq time series experiment on CD4 memory T cells activated with anti-CD3/CD28 beads in individuals with no autoimmune disease. We measured gene expression levels, and allele-specific expression at heterozygous sites over time. We found widespread dynamic genetic regulatory effects across the genome, with an enrichment for genes found in autoimmune disease risk loci. We isolated CD4 memory T cells from PBMC samples of 24 genotyped individuals of European ancestry with no autoimmune disease. We stimulated cells with anti-CD3/CD28 beads and collected cells at 0, 2, 4, 8, 12, 24, 48 and 72 hours. We performed mRNA-seq (TruSeq) for each sample. Samples from 2-4 donors were processed per week. Cells from each donor were plated typically into 8 different wells (with some exceptions), one for each time point, with 1M cells per well to ensure high library complexity. mRNA-seq library preparations happened in 3 plates, donors were randomized over the 3 plates, and samples from the same donor were kept in same plate. For two individuals we performed full time course replicates (from the sample blood draw, CD4 memory T cells were isolated and then separated into 2 independent time course experiments, so in total 16 samples). The sequencing was carried out either with HiSeq 2000 or 2500. However, the submitter does not have the information of which specific Hiseq model each sample was sequenced in. The GEO records have been created with HiSeq 2000 as instrument model for all samples. ***RNA-Seq raw data available through dbGaP (controlled access) due to patient privacy concerns: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002259.v1.p1