|
| Status |
Public on Oct 16, 2019 |
| Title |
Hap1-AS1LV |
| Sample type |
SRA |
| |
|
| Source name |
Hap1-AS1LV
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Hap1
genotype/variation: AS1LV
|
| Growth protocol |
Hap1 cells were cultered in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% FCS (Clontech), 1% Penicillin/Streptomycin (Invitrogen) and 0.5% UltraGlutamin (Lonza). NMuMG cells (Gift of J. Jonkers) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FCS (Clontech), 1% Penicillin/Streptocmycin (Invitrogen) and 0.5% 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 |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
TruSeq libraries prepared from 3C template
4556_6_mitSmc2A_TAGCTT_S6_L001
4556_7_mitSmc2B_GCCAAT_S7_L001
|
| Data processing |
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 |
Jul 19, 2019 |
| Last update date |
Oct 16, 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 (1) |
| GSE108774 |
Distinct Roles for Condensin's Two ATPase Sites in Chromosome Condensation. |
|
| Relations |
| BioSample |
SAMN12322792 |
| SRA |
SRX6475055 |
