|
| Status |
Public on Aug 01, 2017 |
| Title |
RNA pol II Ser2-P ChIP-seq Cdk7as Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116 Cdk7as (Larochelle et al Mol. Cell 25:839, 2007)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
genotype: Cdk7as mutant
antibody: rat monoclonal anti-Ser2-P 3E10 (Chromotek)
|
| Treatment protocol |
WT HCT116 and Cdk7as cells were treated with 10mM NM-PP1 for 24 hr before cross-linking and harvesting for ChIP-seq or RNA-seq
|
| Growth protocol |
McCoy's 10% FCS, 10mM NM-PP1, 24hr
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
cross-linked Chromatin was sonicated with a Bioruptor
1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, gel purification of ~200bp fragments, and amplification (18cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Chromatin IP against RNA pol II Ser2-P
|
| Data processing |
Single-end 50 base reads (after removing barcodes) or 151 base reads (after removing barcodes and trimming adaptor sequences) were mapped to the hg19 UCSC human genome with Bowtie version 0.12.5 for ChIP-seq and with Hisat2 version 2.0.4 for RNA-seq
Genome_build: GRCh37/hg19 assembly
Supplementary_files_format_and_content: bigwig files for ChIP-seq, TDF files for RNA-seq
|
| |
|
| Submission date |
Jun 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
David L. Bentley |
| E-mail(s) |
david.bentley@ucdenver.edu
|
| Organization name |
U. Colorado School of Medicine
|
| Department |
Biochemistry and Mol. Genetics
|
| Street address |
12801 E. 17th Ave
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE100040 |
Human TFIIH kinase CDK7 regulates transcription-associated epigenetic modification |
|
| Relations |
| BioSample |
SAMN07247134 |
| SRA |
SRX2922506 |
