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| Status |
Public on Sep 14, 2016 |
| Title |
MCF7_CTCF_H1 |
| Sample type |
SRA |
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| Source name |
Breast Cancer Cell Line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
treatment: Hypoxia
repeat: 1
chip antibody: CTCF (#07-729, Millipore)
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| Treatment protocol |
For hypoxia treatment cells, were incubated for 16 hr in an In Vivo2 Hypoxia Work station (Ruskinn Technology) at 0.5% oxygen.
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| Growth protocol |
Dulbecco Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100U/ml penicillin and 100 μg/ml streptomycin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq: Cells were fixed with 1% formaldehyde and quenched with glycine (125mM). After washing, cells were lysed (0.5%SDS, 10mM EDTA, 50mM Tris-HCl pH 8.1) and sonicated (Diagenode Biorupter, Belgium). Chromatin was immunoprecipitated using antibodies indicated. Eluted chromatin was heated to reverse cross-linking, treated with proteinase-K, RNaseA and purified on a qiagen PCR pufircation column.
Libraries were prepared using PrepX Complete ILMN DNA library kit (#400076, Wafergen) by the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics, Oxford, UK.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina adaptor sequences were trimmed from the ChIP-seq reads using Trimgalore (0.3.3) and the reads were then aligned to Genome Reference Consortium GRCh37 (hg19) using BWA (0.7.5a-r405)
Low quality mapping was removed (MapQ < 15) using SAMtools (0.1.19) and reads mapping within the Duke Encode black list regions (http://hgwdev.cse.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeMapability) were excluded using BEDTools (2.17.0)
Duplicate reads were marked using Picard tools (1.106) (http://picard.sourceforge.net/) and BigWig files generated for visualization
peaks were identified using T-PIC (Tree shape Peak Identification for ChIP-Seq) and MACS (Model-based analysis of ChIP-Seq)
Genome_build: hg19
Supplementary_files_format_and_content: bed file containing peak calls
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| Submission date |
Feb 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
James Platt |
| Organization name |
University of Oxford
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| Street address |
Roosevelt Drive
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| City |
Oxfors |
| ZIP/Postal code |
OX3 7BN |
| Country |
United Kingdom |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE78113 |
Capture-C reveals preformed chromatin interactions between HIF-binding sites and distant promoters. [ChIP-Seq] |
| GSE78114 |
Capture-C reveals preformed chromatin interactions between HIF-binding sites and distant promoters. |
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| Relations |
| BioSample |
SAMN04504879 |
| SRA |
SRX1594207 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2067526_MCF7_CTCF_H_1_peaks.bed.gz |
726.6 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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