GSM8328315: chimpanzee neurons, differentiated, C3624, 2-week, H3K4me3, rep1  (PLAC-seq); Pan troglodytes; OTHER
2% PFA crosslinked cells comprising 15 μg of genomic DNA were used per PLAC-seq reaction, which corresponds to 4~5 M human or chimpanzee neurons according to estimation. Then the crosslinked chromatin was digested using a restriction enzyme (RE) cocktail followed by the fill-in step of the 5'-overhangs with a biotinylated nucleotide. Next, the spatially proximal digested ends of DNA were ligated while capturing the genomic structure. The proximally-ligated chromatin is then fragmented by sonicator (Covaris S220), immunoprecipitated with anti-H3K4me3 antibody (Millipore 04-745) conjugated Dynabeads (M-280 sheep anti-rabbit IgG, invitrogen #11203D), and purified to yield fragmented proximally-ligated DNA. PLAC-seq was performed according to the protocol from Arima-HiC+ Kit (Arima Genomics, #P/N A101020).