Reference Short-Read Transcriptomes of Activated Human CD4 T cells (Illumina RNA-Seq, Matched to PacBio Iso-Seq Data)
Long-read sequencing technologies such as Iso-Seq (PacBio Inc.) generate highly accurate sequences of full-length mRNA transcript isoforms. Long-read transcriptomics may be especially useful in the context of T cell functional plasticity as it relates to human health and disease. However, To our knowledge, no long-read transcriptome reference exists for activated human CD4 T cells. To begin to fill this gap, we purified CD4 T cells from the peripheral blood of a healthy female donor and activated these cells with anti-CD3/CD28 beads to generate populations of early activated (4hr), mid-activated (16hr), blasting (48hr) and proliferating (120hr) CD4 T cells. From each of these time points, we obtained high-quality RNA (RIN>9) for PacBio Iso-Seq analysis and parallel RNA-Seq analysis, which we hope will serve as a reference for future transcriptomic studies of these populations. UCSC genome browser tracks for these samples can be accessed at: http://genome.ucsc.edu/cgi-bin/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=on&position=chr1:206,903,317-206,921,941&hubUrl=http://162.215.210.70/~tracks/Mitchell_IsoSeq_Stim/hub.txt Overall design: CD4 T cells were enriched to >98% purity from the peripheral blood mononuclear cells of a healthy female donor. Purified CD4 T cells were activated with anti-CD3/CD28 Dynabeads for 4hr (early activated), 16hr (mid-activated), 48hr (blasting) and 120hr (proliferating). RNA was extracted from populations at each time point and used for Pacific Biosciences Iso-Seq long-read sequencing in parallel with Illumina RNA-Seq short-read sequencing. The resulting datasets are offered here as reference transcriptomes for studies of these populations.