GSM9696240: KO; CD8+T; CD3/CD28; Mus musculus; ChIP-Seq
Genomic DNA was extracted under gentle conditions to preserve R-loops. Briefly, cells were lysed in lysis buffer containing SDS and proteinase K and incubated at 37°C overnight. Genomic DNA was then purified by phenol-chloroform extraction followed by ethanol precipitation. The DNA pellet was resuspended in TE buffer. Purified DNA was digested with a cocktail of restriction enzymes (EcoRI, BamHI, HindIII, BsrGI, and XbaI) to generate fragments of approximately 100-500 bp. DNA concentration was determined using a NanoDrop spectrophotometer, and samples were used for subsequent DRIP assays. DNA libraries for DNA-seq were prepared using standard Illumina protocols.