Total Stranded paired end RNA Seq of wildtype and knockout Kdm4a 2 cell embryos

Purpose: The goal of this study was to generate paired-end total RNA Seq transcriptomes of wildtype and Kdm4a 2 cell embryos to study the dynamics of differentially expressed repeats and transposons during early murine development Methods: 2 cell embryos cultured in KSOM EmbryoMax medium (Sigma) were subjected to the SMARTSeq Stranded Total RNASeq protocol according to the manufacturers instructions on the same day simultaneously for control and knockout embryos. Conclusions: Our study represents a detailed analysis of differentially expressed repeats and transposons in embryos lacking maternal or endogenous Kdm4a, with six biologic replicates, generated by SMARTSeq STranded paired end RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that there is a consistent downrgulation of specific LTR families afffected in most biological replicates, by the lack of Kdm4a giving us robust statistical significance. We conclude that Kdm4a is required for proper activation of these repeat elements in conjuction with a permissive chromatin landscape. Total RNA Seq libraries of wildtype and knockout Kdm4a 2 cell embryos using SMARTSeq Stranded kit for single cells with 6 replicates/genotype and sequenced on a high output 75bp paired end Illumina NextSeq 500 platform