 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 27, 2022 |
| Title |
HiC WT |
| Sample type |
SRA |
| |
|
| Source name |
HiC WT rep1
|
| Organism |
Mus musculus |
| Characteristics |
clone: cell line 3G4
cell line: Embyonic stem cell (E14)
treatment: control
|
| Treatment protocol |
Cells were treated with 500 µM auxin (Sigma-Aldrich, I5148-2G) for 0, 90 or 240 min
|
| Growth protocol |
Cells were cultured on gelatin-coated culture plates in Glasgow Minimum Essential Medium (Sigma) supplemented with 15% foetal calf serum (Eurobio Abcys), 1% L-Glutamine (Thermo Fisher Scientific -25030024), 1% Sodium Pyruvate MEM (Thermo Fisher Scientific -11360039), 1% MEM Non-Essential Amino Acids (Thermo Fisher Scientific-11140035) 100 µM β-mercaptoethanol, 20 U/ml leukemia inhibitory factor (Miltenyi Biotec, premium grade), 1 µM MEK inhibitor PDO35901 (Axon, 1408) and 3 µM GSK3 inhibitor CHIR 99021 (Axon, 1386) in 8% CO2 at 37°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% formaldehyde (EMS, 15710) and quenched with 0.125 M glycine for 5min at RT. Cells were lysed in 10 nM Tris-HCl pH 8.0, 10 nM NaCl, 0.2% NP-40 (Sigma-Aldrich, I8896-50ML), complete protease inhibitor (Sigma-Aldrich, 11836170001).
Library preparation was performed according to NEBNext Ultra DNA Library prep kit instruction (NEB, E7370L) and samples were purified with magnetic AMPure bead (Beckman Coulter, A63881).
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
HiC WT rep1
|
| Data processing |
Hi-C paired end datasets were processed using HiC-Pro (version 3.1.0). HiC-Pro covers the whole analysis from fastq files to the interaction matrix
Genome_build: mm9
Supplementary_files_format_and_content: iced and binned matrix (8kb). The format of the matrix is the standard cool matrix format.
|
| |
|
| Submission date |
Feb 22, 2022 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Luca Giorgetti |
| Organization name |
Friedrich Miescher Institute for Biomedical Research
|
| Street address |
Fabrikstrasse 24
|
| City |
Basel |
| ZIP/Postal code |
4056 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE197231 |
Cohesin and CTCF control chromosomal contact dynamics in living cells [Hi-C] |
| GSE197238 |
Cohesin and CTCF control chromosomal contact dynamics in living cells |
|
| Relations |
| BioSample |
SAMN26177816 |
| SRA |
SRX14255704 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5911352_f1.cool.gz |
227.1 Mb |
(ftp)(http) |
COOL |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
