title: GSM6514292: H9 Day 5 Chondrocyte, H3K27ac, bio rep 4 [HiChIP]; Homo sapiens; OTHER
library_construction_protocol: HiChIP experiments were performed following protocol described in (Mumbach et al. 2016) [PMID 27643841], using MboI digestion and sonication using Covaris E220 sonicator with settings power, 140 W; duty factor, 10%; cycle per burst, 200; time, 4 minutes; temp, 4°C, for an intended fragment target size between 200-700bp . For each biological replicate, 10 million CNCCs were fixed in suspension in 1% methanol-free formaldehyde diluted in serum-free medium with end-over-end rotation, quenched with 0.2M Glycine (final concentration), washed twice with ice-cold PBS, pelleted by centrifugation, and snap-frozen in liquid nitrogen. For cranial chondrocytes, cell were fixed similar to CNCCs as either single-cell chondrocytes after ECM digestion according to (Makki et al. 2017) [PMID 28315317], or as undigested "sheets" of chondrocytic tissue, both following 5 days of in vitro differentiation from CNCCs. Libraries were constructed using protocol recommended by NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat No. E7645). We substituted adaptors recommended by this kit with adaptors consisting of unique dual-index barcodes and unique molecular identifiers (IDT xGen UDI-UMI Adapters Cat No 10005925).