Broad existence of pluripotent factor regulated transcript isoforms with stage-specific alternative first exon (SAFE) in mouse embryonic stem cells. Mus musculus

Alternative first exon isoforms are frequently observed among transcriptomes derived from different developmental stages of eukaryotes. Stage-specific alternative first exon (SAFE) transcripts are usually involved in the regulation of cell development in spatiotemporal manners. The transcriptome analysis for RNA-seq data make it possible to identify specifically used first exons in mouse embryonic stem cells (mESCs) compared to somatic cells, just like tail tip fibroblasts (TTFs). In this study, we identify 128 genes producing SAFE isoforms in mESCs. Overall design: mRNA profiles of mouse ESCs and TTFs were generated by deep sequencing using Illumina HiSeq 2000.