GSM6935103: M2_D8_K4me3_S9; Mus musculus; ChIP-Seq
ChIP-seq sample preparation was performed with Covaris kit (PN 520154). Naïve T cells were cultured in vitro under Th9 promoting conditions and treated with chemical cross-linking (1% formaldehyde) on days 0, 3, 4, and 8 (murine) or days 0, 5, 8, and 15 (human). At least 0.5 million cells were used for each immunoprecipitation. After chemical chromatin cross-linking (1% formaldehyde), cells were washed and frozen at -80C. Cells were resuspended in Lysis Buffer B (Covaris) with protease inhibitors, and DNA fragmentation was performed on a Covaris Sonicator (ME220) for 8 min to an average length of 200-700 bp.  After sonication, cells were immunoprecipitated with anti-H3K27Ac (ab4729; Abcam), anti-H3K4Me1 (ab8895; Abcam), and anti-H3K4Me3 (ab8580; Abcam). Genomic DNA (input) was prepared by treating aliquots of chromatin with proteinase K, and heated for de-cross linking, followed by column-based DNA purification (28106, Qiagen).  An aliquot of chromatin underwent immunoprecipitation, after which decrosslinking was performed as above. After recovering purified DNA, 5ng or more of DNA was used to generate libraries using the NEBNext Ultra Directional II DNA sequencing kit per the manufacturer's instructions.