ChIP-seq BL6 primary mouse embryonic fibroblast; 3 lines pooled
background strain
C57Bl/6
cell type
embryonic fibroblast
antibody
ChIP Input pooled chromatin, no antibody.
treatment
control ChIP Input pooled chromatin, no antibody
shRNA
control ChIP Input pooled chromatin
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq assays were performed as described (Rahl et al., 2010, Cell). Briefly, cells were fixed using 1% formaldehyde, harvested, resuspended in ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and sonicated using Covaris water bath sonicator to generate fragments of 150 to 500 bp. Soluble chromatin was diluted 10 fold in ChIP Dilution buffer (1% Triton X-100, 2 mM EDTA pH 8.0, 150 mM NaCl) precleared with Agarose Protein A/G beads (Santa Cruz), and then incuated with antibody specific for total RNA Pol II (N-20, sc-899x, Santa Cruz) or specific for the RNA Pol II Ser5P-phoshorylated form (Abcam #ab5131). After incubation, immunocomplexes were collected with Agarose Protein A/G beads (Santa Cruz). Next, the immunocomplexes were washed sequentially with Low Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), High Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl Wash Buffer (0.25M LiCl, 1% NP40, 1% deoxycholate-Na, 1mM EDTA, 10mM Tris-HCl, pH 8.1) and washed twice with TE (10 mM Tris-HCl pH7.5, 1mM EDTA). Immunocomplexes were eluted in ChIP elution buffer (1%SDS, 0.1M NaHCO3) and the crosslinking was reverted by incubation at 65 ºC for 8 hrs with 200 mM NaCl. Samples were treated with Proteinase K and RNase A ,and DNA was extracted using Phenol-Chloroform. DNA precipitation was in 100% ethanol with 0.1 M NaAcetate ph5.2 and 2 uLs glycogen (Roche). The DNA pellet was washed with 70% ethanol, and resuspended in ddH2O. Purified chromatin was used for library construction. For ChIP-seq the amount of DNA used was ~5 ng from each sample (as quantitated by fluorometry). Samples were were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq DNA Sample Preparation Guide" (part # 15005180 Rev. C). Adapter-ligated libraries were completed by limited-cycle PCR with Q5 High-Fidelity DNA Polymerase (NEB) and Illumina PE primers (15 cycles), and further purified with a double-sided SPRI size selection to obtain a size distribution in the range of 230-500bp. Libraries were applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.