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.

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.