RNA sequencing of blastocyst-stage mouse embryos in the presence or absence of RNA decay activator UPF2

Purpose: The goal of this study is to compare transcriptome profiles of whole blastocysts in the presence or absence of UPF2, via an approach optimized for low-input samples. Methods: Blastocyst mRNA profiles of wild-type (WT) and Upf2 knockout (Upf2−/−) mice were generated by deep sequencing, using Illumina 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with DESeq2 and with IsoformSwitchAnalyzeR. Results: We identified transcripts targeted for decay by UPF2 and the NMD pathway in the blastocyst via multiple methods. We found that NMD regulates a cohort of RNAs involved in cell survival. Blastocyst-stage embryo RNA profiling in Upf2−/− and WT mice.