title: Chd5 mouse chip-seq
design: Chromatin was prepared from wild-type mefs and used for immunoprecipitation. ChIP analyses were performed as described previously (Zeng et al., 2006) with some modifications. 1X107 cells were used per immunoprecipitation and were sequentially cross-linked with ethylene glycolbis[succinimidyl succinate] (EGS) (Thermo Scientific) for 30 m, followed by 1% formaldehyde for 10 m at room temperature. Cross-linking was quenched with glycine, cells were washed, lysed, and chromatin was sheared using sonication. Chromatin was immunoprecipitated with Dyna-beads pre-conjugated with primary antibodies specific for normal rabbit IgG, Chd5 (M-182), or H3K4me3. The immunoprecipitated samples were washed, eluted, and cross-linking was reversed with 200 mM NaCl for 8 hrs. Samples were RNase A digested and proteinase K treated before phenol/chloroform extraction, and samples were used for ChIP-Solexa sequencing (performed at the CSHL Genomics Shared Resource) or for quantitative PCR (qPCR). Samples were analyzed in triplicate by real-time PCR using SYBR green (Quanta Biosciences) on the LightCycler 480 (Roche). To allow comparison among primer sets, unprecipitated input samples from each condition were serially diluted and used as standards for all PCRs.