GSM1163125: RNAP_Ser5_Phos_MES_Rep_2; Mus musculus; ChIP-Seq
Altered sonication and wash buffers used for this sample as described in Rahl et al., 2010 Chromatin immunoprecipitation of histone modifications were performed according to the Young lab protocol (Lee et al., 2006) with minor modification. Briefly, frozen pellets of cross-linked cells (10 3 106) were thawed in cold lysis buffer 1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1 3 protease inhibitors) and gently rocked at 4  C for 10 min in 14 ml conical tubes. Cells were pelleted at 1350 x g at 4 C in a clinical centrifuge and resuspended in cold lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1 3 protease inhibitors) and gently rocked at 4 C for 10 min in 14 ml conical tubes. Cells were pelleted at 1350 x g at 4C in a table top centrifuge and resuspended in 2 ml cold lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1 3 protease inhibitors) and sonicated to 200-600 bp fragments using a Diagenode Bioruptor (3 3 10 min cycles, 30 s ON / 30 s OFF at 4 C). Soni- cated lysates were cleared by pelleting insoluble material at 20,000 x g at 4  C followed by incubation with antibody bound Protein A/G magnetic beads (2.5 mg Ab / 50uL beads / IP) in 1 ml of 0.5% BSA/PBS overnight at 4 C. Magnetic beads were washed 3 times with block (0.5% BSA/PBS), incubated for approximately 4 hr at 4 C with antibody in block and then washed 3 times with block prior to addition of cleared cell lysates. Immunoprecipitated material was washed five times with cold wash buffer (RIPA: 50 mM HEPES-KOH, pKa 7.55, 500 mM LiCl, 1 mM EDTA, 1.0% NP-40, 0.7% Na-Deoxycholate) and one time with TE plus NaCl, followed by elution and uncrosslinking in 210 uL of 1% SDS in TE overnight at 65  C. 200 uL of uncrosslinked material was treated with RNase A for 2 hr, proteinase K for 2 hr and extracted 2 times with phenol chloroform isoamyl alcohol, followed by ethanol precipitation with a glycogen coprecipitant, 80% ethanol wash and final resuspension in TE. Illumina sequencing libraries were generated (Schmidt et al., 2009), with minor modi- fication. Briefly, 5-50 ng of immunoprecipitated nucleic acid was end repaired, a-tailed and ligated to Illumina single end adapters using an NEB Next kit (New England Biolabs).  200-300 bp adaptor ligated nucleic acid was gel purified and enriched via 19 cycles of PCR amplification with Phusion High-Fidelity DNA Polymerase, followed by sequencing on an Illumina HiSeq 2000 system
GEO Accession
GSM1163125