Integrating Genomics, Transcriptomics, and T-Cell Biology: An RNA-seq Atlas of the Murine CD4+ Transcriptome

CD4+ cells are key regulators of the adaptive immune system and can be classified into two main groups: T helper cells (naive, Th1, Th2 and Th17 cells), and regulatory T cells, iTreg and nTreg cells). We performed mRNA-sequencing on these major CD4+ cell subtypes, and integrated multiple computational methods for analyzing gene/isoform expression, differential expression, and functional annotation. Our primary analysis not only provides evidence for the very high quality of the sequence data, but also reveals novel patterns of read distributions inside and adjacent to genes. We identify 168 novel transcripts, which are differentially expressed in the various CD4+ cell subtypes. Further, we identify a wealth of novel, uniquely differentially expressed ''signature'' transcripts for each cell type. nTreg cells have the largest number of these, with 477 signature genes in total, of which 58 are transcription factors. The data is compiled into an easily accessible online database publically available at http://www.thelpercell.com. Overall design: RNA-seq data of Murine CD4+ cells