|
| Status |
Public on Mar 14, 2022 |
| Title |
∆HDAC8 Asynchronous Replicate 1 HiC |
| Sample type |
SRA |
| |
|
| Source name |
HAP1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HAP1
genotype: {delta}HDAC8
|
| Treatment protocol |
CRISPRs targeting ESCO1 (5’-CATGAGTACAAGGTCATCAA-3’ and 5’-AGCTTAACCGGAGATCACAA-3’), HDAC8 (5’-CAGTGGGCAGTCGCTGGTCC-3’ and 5’-CGGGACTATAGATATAAACC-3’), PDS5A (5’-GTGGCGTCGTGAGTGCCGACGGG-3’ and 5’-GGAAGATCGCTTACCCTCCG-3’), and PDS5B (5’-TCTGATATTTCCTTGACCCC-3’) were cloned into px330 (Addgene plasmid #42230). ∆WAPL cells were generated before (Haarhuis et al., 2017), and used as a parental cell line to generate double knockout cells for WAPL and ESCO1. Either blasticidine or puromycin resistance cassettes were used, as described previously (Blomen et al., 2015). Knockout cell lines were confirmed by PCR genotyping and Western Blotting Analysis.
|
| Growth protocol |
HAP1 cells (Carette et al., 2011) were cultured in Iscove’s modified Dulbecco’s medium (Invitrogen), supplemented with 10% FCS (Clontech), 1% UltraGlutamin (Lonza) and 1% penicillin-streptomycin (Invitrogen).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C libraries were prepared as previously described (Rao et al., 2014). The protocol was adapted slightly for G1 analyses. An asynchronous pool of cells was first crosslinked using 2% formaldehyde. Then the 10% smallest cells were sorted based on Forward Scatter and Side Scatter. 5 million cells were collected for Hi-C analysis and then processed according to protocol following crosslinking.
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 |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
∆HDAC8 Asynchronous Replicate 1
|
| Data processing |
Raw sequence data was mapped and processed using HiC-Pro v2.9 (Servant et al., 2015).
Genome_build: hg19
Supplementary_files_format_and_content: .hic file (contains contact matrices at various resolutions).
|
| |
|
| Submission date |
Nov 02, 2021 |
| Last update date |
Mar 14, 2022 |
| Contact name |
Angela Sedeno Cacciatore |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
Netherlands Cancer Institute
|
| Department |
Gene regulation
|
| Lab |
Rowland lab
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| State/province |
Noord-Holland |
| ZIP/Postal code |
1066 CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE150564 |
The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism (Hi-C) |
| GSE174628 |
The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism |
|
| Relations |
| BioSample |
SAMN22841073 |
| SRA |
SRX12905903 |
