title: ChIP_MSQ43_input_Rep2
design: This ChIP-seq experiment began with 2030 million MSQ43 cells fixed using 1% paraformaldehyde for 15 minutes at room temperature to cross-link proteins to DNA, followed by glycine quenching. Cells were lysed in a buffer containing 10 mM Tris-HCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, protease inhibitors, and 0.5% SDS , and chromatin was isolated via sonication (Bandelin Sonopulse, 75% power, 8 cycles) and quantified using Qubit. For input control generation, 2040 g of chromatin was reserved prior to immunoprecipitation, diluted to 0.10.2% SDS in lysis buffer, and processed identically to ChIP samples. Cross-links were reversed by incubating at 65C for 14 hours with RNase A and Proteinase K to remove RNA and protein contaminants. DNA was purified using Zymo ChIP DNA Clean & Concentrator columns , eluted in TE buffer, and used to prepare libraries with the KAPA Hyper Prep Kit (Roche) for sequencing on the DNBSEQ platform .