title: GSM5093511: D7 ES CHART-seq input, rep3; Mus musculus; OTHER
library_construction_protocol: CHART-seq: Cells were crosslinked with 1% formaldehyde and nuclei were further crosslinked with 3% formaldehyde. Nuclei chromatin was sheared by sonication to yield the majority of fragments with approximately 3kb. The resulting extracts were hybridized with either Jpx CHART probes (biotinylated DNA oligonucleotides that were complementary to Jpx) or Jpx AS CHART probes (the reverse complement of Jpx CHART probes) and then captured by streptavidin beads. After washes, DNA was eluted in the elution buffer with RNase H. No-RNaseH CHART was generated from Jpx CHART eluant in the absence of RNase H. CHART enriched DNA was further sonicated and subjected to library construction steps using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S) for Illumina.