We have determined the transcriptomes of six tissues comprising the entire TS12 (E8.25) mouse embryo using massively parallel sequencing. We present an unprecedented, tissue-specific and global transcriptome analysis.. The transcriptomic landscape of the TS12 mouse embryo determined by massively pa

Differential gene expression is a prerequisite for the formation of multiple cell types from the fertilized egg during embryogenesis. Understanding the gene regulatory networks controlling cellular differentiation requires the identification of crucial differentially-expressed control genes and, ideally, the determination of the complete transcriptomes of each individual cell type. Here, we have analyzed the transcriptomes of six major tissues dissected from midgestational (TS12) mouse embryos. Approximately one billion reads derived by RNA-seq provided extended transcript lengths, novel first exons and alternative transcripts of known genes. We have identified 1,375 genes showing tissue-specific expression, providing gene signatures for each of the six tissues. In addition, we have identified 1,403 novel potential noncoding RNA loci, 439 of which show differential expression. Our analysis provides the first transcriptome data for the mouse embryo based on massively parallel sequencing. It offers a rich data source for the analysis of individual genes and gene regulatory networks controlling midgestational development.差异基因表达是胚胎发生过程中受精卵发育形成多种细胞类型的必要前提。解析调控细胞分化的基因调控网络，需要鉴定关键的差异表达调控基因，理想情况下还需明确每一种单一细胞类型的完整转录组（transcriptome）。本研究针对妊娠中期（TS12）小鼠胚胎的六大主要解剖组织开展转录组分析：通过RNA测序（RNA-seq）获得约10亿条测序读段（reads），这些数据延伸了已知基因的转录本长度，同时发现了全新的第一外显子以及已知基因的可变剪接转录本。我们共鉴定出1375个具有组织特异性表达的基因，可为这六大组织分别提供基因特征（gene signature）。此外，本研究还鉴定出1403个潜在的新型非编码RNA基因座（noncoding RNA loci），其中439个呈现差异表达特征。本研究基于大规模并行测序技术，首次获取了小鼠胚胎的转录组数据，该数据集为解析调控妊娠中期胚胎发育的单个基因及基因调控网络提供了丰富的数据资源。