|
| Status |
Public on Mar 07, 2024 |
| Title |
DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at different times: 3-8hr DMSO R1 |
| Sample type |
SRA |
| |
|
| Source name |
uterine/cervical adenocarcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa-S3 (CCL-2.2)
tissue: uterine/cervical adenocarcinoma cell line
|
| Treatment protocol |
Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. DMSO was added at t3hr, and cells were fixed at t8hr. G1 cells were isolated by FACS.
|
| Growth protocol |
HeLa-S3 cells were cultured in glutamax DMEM supplemented with 10% heat-inactivated FBS and penicillin-streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For each Hi-C library, approximately 1-5 million cells were used as input. Cells were crosslinked for 10 minutes at room temperature in a final concentration of 1% formaldehyde. Glycine was added to quench crosslinking. Cell pellets were frozen at -80C until PI staining and cell sorting, then were again frozen and stored at -80C until Hi-C library generation.
Hi-C was performed as described in Belagzhal et al, 2017, Methods. Restriction enzyme: DpnII
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Fastq files were mapped to the hg38 genome using the distiller pipeline (github.com/mirnylab/distiller-nf). Hi-C interaction data was stored in the cooler format (Abdennur, N., and Mirny, L. (2019). Reads were filtered for mapping quality (>Mapq30), and read normalized within each experiment. Multiresolution cooler files with iterative correction were made for both individual replicates and combined replicates.
Multiresolution cooler files (multires.cool) containing high quality (Mapq>30) read normalized pairwise interactions for separate replicates and combined replicates.
Assembly: hg38
|
| |
|
| Submission date |
Mar 14, 2022 |
| Last update date |
Mar 07, 2024 |
| Contact name |
Job Dekker |
| E-mail(s) |
job.dekker@umassmed.edu
|
| Organization name |
University of Massachusetts Medical School/HHMI
|
| Department |
Program in Systems Biology
|
| Lab |
Dekker Lab
|
| Street address |
368 Plantation Street
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01606 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE198610 |
Mitotic chromosomes are self-entangled and disentangle through a Topoisomerase II-dependent two stage exit from mitosis |
|
| Relations |
| BioSample |
SAMN26660497 |
| SRA |
SRX14464204 |
