Genome-wide Kdm1a binding in X chromosome by high throughput sequencing [ChIP-Seq]

We analyzed KDM1A (LSD1) occupancy in 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 distiguish genome DNA from the Xi. We found a possible physical and/or functional regulation of KDM1A during the X chromosome reactivation in the intiation site on the Xi. Chromatins were isolated from MEF, and cells reprogrammed by SeVdp(fKOSMaB) with or without 30 nM Shield1 at day 20. ChIP was performed using anti-LSD1 antibody (ab17721, abcam). Libraries were sequenced on an Illumina NovaSeq 6000 and data was analyzed allele-specifically by variantcall using bcftools mpileup.