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. 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.