The tissue-specific transcriptomic landscape of the mid-gestational mouse embryo
- 1 June 2014
- journal article
- Published by The Company of Biologists in Development
- Vol. 141 (11), 2325-2330
- https://doi.org/10.1242/dev.105858
Abstract
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 mid-gestational (TS12) mouse embryos. Approximately one billion reads derived by RNA-seq analysis provided extended transcript lengths, novel first exons and alternative transcripts of known genes. We have identified 1375 genes showing tissue-specific expression, providing gene signatures for each of the six tissues. In addition, we have identified 1403 novel putative long noncoding RNA gene loci, 439 of which show differential expression. Our analysis provides the first complete transcriptome data for the mouse embryo. It offers a rich data source for the analysis of individual genes and gene regulatory networks controlling mid-gestational development.Keywords
This publication has 27 references indexed in Scilit:
- Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissuesF1000Research, 2013
- STAR: ultrafast universal RNA-seq alignerBioinformatics, 2012
- The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expressionGenome Research, 2012
- An integrated encyclopedia of DNA elements in the human genomeNature, 2012
- Web-based digital gene expression atlases for the mouseMammalian Genome, 2012
- A User's Guide to the Encyclopedia of DNA Elements (ENCODE)PLoS Biology, 2011
- A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse EmbryoPLoS Biology, 2010
- miRBase: microRNA Sequences and AnnotationCurrent Protocols in Bioinformatics, 2010
- Mouse Brain Organization Revealed Through Direct Genome-Scale TF Expression AnalysisScience, 2004
- Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profilesBioinformatics, 2003