Genome-wide transcripts from X chromosome by high throughput sequencing [RNA-Seq]

We analyzed a transcriptional landscape of the Xi during somatic cell reprogramming of female mouse cells. We use MEFs from hybrid embryos by crossing male Mus spretus and female Mus musculus domesticus C57BL/6J to monitor allele-specific transcripts from the Xi. We could capture the earliest phase of X chromosome reactivation and found that a subset of genes clustered near the centromere display an early reactivation on the Xi. Overall design: RNA were isolated from MEF, and cells reprogrammed by SeVdp(fKOSMaB) with or without 30 nM Shield1. Libraries were sequenced on an Illumina NextSeq500 with paired-end mode for 2x76-base reads. Data was analyzed allele-specifically by variantcall using Basic Variant Call tool in CLC-Genomic Workbench.