|
| Status |
Public on May 03, 2017 |
| Title |
SCC4KO-C Hi-C |
| Sample type |
SRA |
| |
|
| Source name |
Hap1 SCC4KO
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Hap1
genotype/variation: SCC4KO
|
| Treatment protocol |
CRISPRs targeting WAPL (5’-CACCGCGTTCCATAGTATCCTGTA-3’) and SCC4 (5’-CACCGTACGGGCCTCGATGCGCTG-3’) were cloned into px330 (Addgene plasmid #42230). ∆WAPL and ∆SCC4 HAP1 clones were generated by insertion of a Blasticidine or Puromycin cassette respectively, as previously described (Blomen et al., 2015). ∆WAPL/∆SCC4 cells were generated by knocking out SCC4 in ∆WAPL cells.
|
| Growth protocol |
HAP1 cells (Carette et al., 2011) were cultured in IMDM (Invitrogen) supplemented with 10% FCS (Clontech), 1% Penicillin-Streptomycin (Invitrogen) and 1% Ultraglutamin (Lonza).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C was performed essentially as previously described (Rao et al., 2014). Briefly, for each template roughly 10 million cells were crosslinked using 2% formaldehyde. In nucleus restriction was performed using MboI. Restriction overhangs were filled in with biotinylated nucleotides followed by blunt-end ligation. A streptavidin pull-down was performed to enrich for ligated sequences.
Pulled-down DNA was end-repaired and an A-overhang was added. Sequencing adapters were ligated to the DNA samples to create sequencing libraries.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
TruSeq libraries prepared from 3C template
SCC4KO.validPairs
|
| Data processing |
Library strategy: HiC-Seq
Raw sequence data was mapped and processed using HiC-Pro v2.7.7 (Servant et al., 2015).
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C summary files contain the genomic position and strand of the two pairs of a Hi-C ligation
|
| |
|
| Submission date |
Feb 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Robin H. van der Weide |
| Organization name |
Hubrecht Institute
|
| Lab |
Kind Lab
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE95014 |
The cohesin release factor WAPL restricts chromatin loop extension. [HiC-Seq] |
| GSE95015 |
The cohesin release factor WAPL restricts chromatin loop extension. |
|
| Relations |
| BioSample |
SAMN06344498 |
| SRA |
SRX2570676 |
