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Sample GSM1670715 Query DataSets for GSM1670715
Status Public on Oct 01, 2015
Title HuCCT1 ps5 Pol2 siRNA YAP/TAZ
Sample type SRA
 
Source name HuCCT1 human cell line
Organism Homo sapiens
Characteristics cell line: HuCCT1
sirna: YAP/TAZ
chip antibody: Phospho-Rpb1 CTD (Ser5) (Cell Signaling, catalog# 13523, lot# 1)
Extracted molecule genomic DNA
Extraction protocol Cells were cross-linked in 1% formaldehyde for 10 minutes at room temperature after which the reaction was stopped by addition of 0.125M glycine. Cells were lysed and harvested in ChIP buffer (100 mM Tris at pH 8.6, 0.3% SDS, 1.7% Triton X-100 and 5 mM EDTA) and the chromatin disrupted by sonication using a Diagenode Bioruptor sonicator UCD-200 to obtain fragments of 200-500 bp in size. Suitable amounts of chromatin were incubated with specific antibodies overnight. Antibodies used are: H3K4Me3 (Millipore – Cat. # 07-473), H3K27Ac (Abcam – Cat. # ab4729), H3K4Me1 (Abcam – Cat. # ab8895), MED1 (Bethyl – Cat. # A300-793A), SMC1 (Bethyl – Cat. # A300-005A), Pol2 (Santa Cruz – Cat. # sc-899), Phospho-Rpb1 CTD (Ser2) (Cell Signaling – Cat. # 13499), Phospho-Rpb1 CTD (Ser5) (Cell Signaling – Cat. # 13523), CDK9 (Santa Cruz – Cat. # sc-484)
Libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina and barcoded using NEBNext Multiplex Oligos for Illumina according to manufacturer recommendation.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Reads have been aligned against Human reference genome hg19 using Bowtie2 aligner with default parameters. Aligned reads have been used either for coverage evaluation (normalized by library size) stored in bigWig format or for peak-calling procedures using MACS software (version 1.3.7.1) with a lower enrichment cutoff of 5 (mfold=5) and a pvalue cutoff of 10e-08
in order to find regions for significant coverage enrichment. IgG signal has been used to model the background noise for all datasets analyzed with MACS..
Genome_build: hg19
Supplementary_files_format_and_content: bed file containing the genomic positions of the significant peaks output by MACS. BigWig file containing normalized coverage data
 
Submission date Apr 29, 2015
Last update date May 15, 2019
Contact name Raffaele A Calogero
E-mail(s) raffaele.calogero@unito.it
Phone ++39 0116706454
Organization name University of Torino
Department Molecular Biotechnology Center
Lab Bioinformatics and Genomics Unit
Street address Via Nizza 52
City Torino
State/province To
ZIP/Postal code 10126
Country Italy
 
Platform ID GPL11154
Series (2)
GSE62275 YAP drives proliferation and tumorigenesis by recruiting Mediator to super- enhancer elements
GSE68388 YAP drives growth by controlling transcriptional pause release from dynamic enhancers (HuCCT1_siRNA)
Relations
BioSample SAMN03571595
SRA SRX1013340

Supplementary file Size Download File type/resource
GSM1670715_hucct1_ps5_siyt.bw 279.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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