Transcriptional dysregulation associated with chromatin accessibility of iPSC and hepatocytes derived from a Cornelia de Lange syndrome patient (ChIP-Seq)
Transcriptional dysregulation associated with chromatin accessibility of iPSC and hepatocytes derived from a Cornelia de Lange syndrome patient (ChIP-Seq)
Briefly, 2-3x107 cells were harvested, fixed with 1 % formaldehyde and quenched with 125 mM glycine. Fixed cells were lysed and the nuclei were extracted. The size of the DNA fragments were adjusted to 300-900 bp long by sonication in the BioRupter sonicator (Diagenor). Immunoprecipitation was performed using the whole genome extracts derived from the cells equivalent to 5x106 cells and 10 g of antibody.  The antibodies used were; H3K4me3 (39159, Active Motif), acetylK27 (ab4729, Abcam), NIPBL (A-301-779A/A-301-778A, Bethyl Laboratories), CTCF (07-729 Merck/348S Cell Signaling), RAD21 (ab952, Abcam/4321S, Cell Signaling).  Small DNA fragments and antibody-protein complexes were purified using protein-G conjugated DynaBeads (Invitrogen). The DNA fragments were reverse-crosslinked and purified by QIAquick PCR purification kit (Qiagen).