|
| Status |
Public on Jul 13, 2020 |
| Title |
CTCF depleted R2 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa CTCF SCC1 AID
|
| Organism |
Homo sapiens |
| Characteristics |
strain: Kyoto
type: +Auxin
treatment: treatment
|
| Treatment protocol |
SCC1 and CTCF depleted cells were treated with Auxin, G1 and G2 cells were synchronised with thymidine, Mitotic cells were synchronised with nocodazole, RNAi samples were treated simultaneously with appropriate shRNAs for WAPL, PDS5A and PDS5B
|
| Growth protocol |
Cells were cultured at 37 degrees C in suspension in DMEM supplemented with 10% FCS, glutamate and penicillin-streptavidin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
HindIII-based Hi-C libraries were captured using SureSelect target enrichment system, using a custom-designed RNA bait library and paired-end blockers. Promoter-based ligated products were isolated and amplified
PCHiC libraries were constructed using HindIII as described in (Schoenfelder et al. 2018 and Wutz et al. 2017).
PCHiC
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PCHiC
|
| Data processing |
QC: FastQC & FastQscreen
Pre-processing: HiCUP
Processing: ChiCAGO
Genome_build: GRCh37
Supplementary_files_format_and_content: .Rds serialized R objects
|
| |
|
| Submission date |
Feb 21, 2020 |
| Last update date |
Jul 14, 2020 |
| Contact name |
Michiel Johannes Thiecke |
| Organization name |
Babraham research institute
|
| Department |
Nuclear dynamics
|
| Lab |
Spivakov
|
| Street address |
Babraham Hall
|
| City |
Cambridge |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB22 3AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE145735 |
Cohesin-dependent and independent mechanisms support chromosomal contacts between promoters and enhancers (PCHiC) |
| GSE145736 |
Cohesin-dependent and independent mechanisms support chromosomal contacts between promoters and enhancers |
|
| Relations |
| BioSample |
SAMN14162388 |
| SRA |
SRX7779351 |
