|
| Status |
Public on Oct 01, 2015 |
| Title |
HuCCT1 CDK9 siRNA Control |
| Sample type |
SRA |
| |
|
| Source name |
HuCCT1 human cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HuCCT1
sirna: Control
chip antibody: CDK9 (Santa Cruz, catalog# sc-484, lot# I0414)
|
| 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 |
SAMN03571596 |
| SRA |
SRX1013341 |
