|
| Status |
Public on Mar 07, 2024 |
| Title |
DpnII MC-3C on HeLa S3 MR: 2-4hrs ICRF-193 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. 30uM ICRF-193 was added at t2hr, and cells were fixed at t4hr. 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 MC-3C 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. Cells were then crosslinked with 3mM DSG for 45 minutes at room temperature, and DSG crosslinking was quenched with Tris. Cell pellets were frozen at -80C until PI staining and cell sorting, then were again frozen and stored at -80C until MC-3C library generation.
MC-3C was performed as described in Tavares-Cadete and Norouzi et al, Nature Structural and Molecular Biology. Restriction enzyme: DpnII
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| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Sequel II |
| |
|
| Data processing |
Library strategy: MC-3C
PacBio SMRTLink software was used to call circular consensus sequences (CCS). Fastq files containing CCS were mapped to the hg38 genome using minimap2. Mapped C-walks were then annotated both at the fragment and the C-walk level for further filtering and analysis, including number of fragments per C-walk, number of chromosomes and compartment types visited, proximity of each fragment to the largest step in each C-walk, the size of the largest step for each C-walk, the distance of each direct pairwise interaction, the total span of each C-walk, and other features.
Tab delimited text file containing mapped and annotated C-walks. All HeLa S3 samples are combined in one processed data file. The table contains the first 2-10 fragments of all C-walks, organized based on number of fragments. Note that there is overlap between the length classes, e.g. 2 fragment C-walks in this table include C-walks with only 2 fragments as well as the first 2 fragments of C-walks 3 fragments and longer, etc.
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 |
GPL28352 |
| Series (1) |
| GSE198610 |
Mitotic chromosomes are self-entangled and disentangle through a Topoisomerase II-dependent two stage exit from mitosis |
|
| Relations |
| BioSample |
SAMN26660401 |
| SRA |
SRX14464266 |
