title: GSM7213672: MSX1FNV, 3h dTAG, rep1, H3K27ac; Homo sapiens; ChIP-Seq
library_construction_protocol: Cells (about 1 confluent 10-cm plate or ~10-20 million cells) were crosslinked with 1% methanol-free formaldehyde (Pierce, 28908) in PBS for 10 min at room temperature and then quenched by adding 2.5 M glycine to 125 mM final concentration and incubating for 10 min. Cells were washed in PBS with 0.001% v/v Triton X-100, harvested by scraping, and collected by centrifugation for 5 min at 4°C. Cells were washed with PBS and flash frozen for storage at -80°C. Cell pellets were later thawed on ice for 30 min, and then sequentially resuspended in lysis buffer 1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% Igepal CA-630, 0.25% Triton X-100, 1x cOmplete EDTA-free protease inhibitor cocktail (PIC), 1 mM PMSF), lysis buffer 2 (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x cOmplete EDTA-free protease inhibitor cocktail, 1 mM PMSF), and lysis buffer 3 (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine, 1x PIC, 1 mM PMSF), with 10 min incubations in each buffer, with rotation. Lysates were sonicated for 10-15 cycles of 30s ON/30s OFF on high power using the Bioruptor Plus (Diagenode), then diluted in additional lysis buffer 3 and clarified by centrifugation for 10 min at max speed at 4°C. Triton X-100 was added to 1%, and a small aliquot was used to extract DNA to check chromatin yield and size distribution, by dilution in elution buffer (1% w/v SDS and 100 mM NaHCO3) and incubation with 200 mM NaCl and RNase A (Thermo, EN0531) at 65°C for 1 h, then proteinase K (Thermo, EO0491) at 65°C for 1 h, and clean up with the ChIP DNA Clean & Concentrator-5 kit (Zymo, D5205). DNA was quantified by Qubit dsDNA high sensitivity kit, and the remaining chromatin was then normalized for immunoprecipitations. For TWIST1 acute depletions, chromatin from O9-1 mouse CNCCs were added prior to ChIP at ~10% of the total chromatin as a spike-in control. For H3K27ac, 5 ug of antibody was used per ChIP; for TFs, 9 ug of antibody was used per ChIP, except for dissected mouse embryos where 4.5 ug was used in half of the total ChIP volume. ChIPs were incubated overnight, then incubated for 4-6h with 100 ul Dynabeads Protein A (Invitrogen, 10002D) or Protein G (Invitrogen, 10004D) prewashed with 0.1% w/v BSA in PBS, then washed 5x with RIPA wash buffer (50 mM HEPES-KOH pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% Igepal CA-630, 0.7% w/v sodium deoxycholate), once with 50 mM Tris-HCl pH 8, 10 mM EDTA, 50 mM NaCl, and eluted in elution buffer at 65°C for 30 min. Eluate was then reverse crosslinked and treated with RNase A and proteinase K, and then DNA was extracted with the ChIP DNA Clean & Concentrator-5 kit. Libraries were prepared using the NEBNext Ultra II DNA kit (New England Biolabs, E7645S) using up to 50 ng of input or ChIP DNA, with ~4-8 cycles of amplification, with no pre-PCR size selection but a post-PCR double-sided 0.5x/0.9x Ampure XP bead clean-up.