GSM1973770: BMSC_d21_h3k9ac_R2; Mus musculus; ChIP-Seq
Chromatin were prepared and sheared as previously described [12]. Sheared chromatin was used for immunoprecipitation with Runx2 antibody (M-70, Santa Cruz), Ctcf (07-729, Millipore, Billerica, MA, USA), Smc1a (A300-055A, Bethyl Laboratories, Montgomery, TX, USA), H3K4me (ab8895, Abcam, Cambridge, MA, USA), H3K4me3 (ab1012, Abcam), H3K9me3 (Ab8898, Abcam), H3K9ac (39137, Active Motif), H3K27me3 (07-449, Millipore), H3K27ac (07-360, Millipore), H3K36me3 (ab9050, Abcam), ap300 (sc-585 X, Santa Cruz) or Ezh2 (A304-196A, Bethyl Laboratories) or immunoglobulin G (IgG) (12-370, Millipore) followed by purification using Protein-G Dynabeads (Invitrogen). Briefly, end-repair, A-tailing and paired-end adapter ligation were performed using 8 ug of ChIP-DNA at 150 pg/ul using the TruSeq ChIP sample preparation kit (Illumina cat#9235121 lot #15027084) following manufacture’s instructions. Excess adapters were removed by sequential Ampure XP (Beckman Coulter A63881 lot #1348300) purifications and recovered, ligated fragments were the amplified by PCR on a Biorad thermal cycler. Libraries were then run on a 2% agarose/TAE gel to select for fragments in the 350-400 bp range. Libraries were sequenced on an Illumina GA-II or Hiseq1500 and single-end 36-base (SE36) sequencing was performed at the NEMO facility at Umass Medical School