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 publicly available at http://www.thelpercell.com. RNA-seq data of Murine CD4+ cellsCD4+细胞是适应性免疫系统的关键调节因子，可划分为两大类别：辅助性T细胞（涵盖初始T辅助细胞、Th1、Th2及Th17细胞）与调节性T细胞（包括iTreg与nTreg细胞）。本研究针对上述主要CD4+细胞亚型开展了mRNA测序（mRNA-sequencing），并整合多种计算方法以分析基因/转录本异构体表达、差异表达情况及功能注释。本研究的初步分析不仅证实了测序数据的极高质量，还揭示了基因内部及基因邻近区域的测序读段分布新模式。本次研究共鉴定出168个全新转录本，这些转录本在不同CD4+细胞亚型中呈差异表达。此外，本研究还为每种细胞类型鉴定出大量全新的、特异性差异表达的“特征”转录本。其中nTreg细胞的此类特征转录本数量最多，总计包含477个特征基因，其中58个为转录因子。相关数据已整理为易于访问的公开在线数据库，访问地址为http://www.thelpercell.com。本数据集包含小鼠CD4+细胞的RNA测序（RNA-seq）数据。