GSM9421090: RA_0d-rep2; Mus musculus; OTHER
ESCs were lysed with Trizol reagent (Life Technologies), and RNA was extracted based on the manufacturer's instructions. Crosslink & isolate nuclei: Fix cells with formaldehyde, quench, and prepare nuclei.  Digest chromatin: Cut DNA in nuclei with a restriction enzyme (commonly MboI/DpnII).  Fill-in + biotin label: Fill ends with biotinylated nucleotides.  Proximity ligation (in situ): Ligate DNA ends in nuclei to capture 3D contacts.  Shear DNA: Sonicate to ~200–500 bp fragments.  ChIP enrichment: Immunoprecipitate chromatin using an antibody to the target protein/mark (e.g., H3K27ac).  Reverse crosslinks & purify DNA: Proteinase digestion, clean up DNA.  Pull down biotin DNA: Enrich ligation junctions with streptavidin beads.  End repair / A-tailing / adapter ligation: Prepare fragments and ligate sequencing adapters.  PCR amplify & QC: Limited-cycle PCR, size selection if needed, quantify, then paired-end sequencing.