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Sample GSM2670990 Query DataSets for GSM2670990
Status Public on Aug 01, 2017
Title HCE ChIP-seq Cdk7as Rep1
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: rabbit anti-HCE (Glover-Cutter et al NSMB. 15:71, 2008)
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 human capping enzyme
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 SAMN07247140
SRA SRX2922509

Supplementary file Size Download File type/resource
GSM2670990_hg19_Cdk7AS_3MB_HCE_BC6G6KANXX_R1_TCAAGT.bw 257.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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