GSM4007490: RNAseq, ES_RepB, Day10; Mus musculus; RNA-Seq
ChIP-seq: Cells were crosslinked with 1% formaldeyde for 10 min, then nuclei were isolated and lysed. Chromatin was sheared by sonication to a size of ~200-400 bp. Cleared lysates were precleared for 1 hour, then 10% saved as input, and lysates were incubated with Dynabeads Protein G pre-bound with the antibody of choice. After stringent washes, ChIP DNA was eluted from beads, and together with input chromtain was reverse-crosslinked with proteinase K. DNA was purified by phenol/chloroform extraction and ethanol precipitation. RNA-seq: Total cell RNA was extracted using TRIzol (Thermo Fisher), from which mRNA was isolated using oligo(dT) beads and RNA-seq libraries prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) as per manufacturer's instructions. Libraries were constructed using the NEBNext ChIP-seq Library Preparation Kit with no modifications to the protocol. We used 9-14 cycles of PCR amplification, depending on library concentration measured by qPCR.