|
Status |
Public on Feb 27, 2022 |
Title |
cell line 3G4 90min treatment rep1 |
Sample type |
SRA |
|
|
Source name |
3G4 90min treatment
|
Organism |
Mus musculus |
Characteristics |
clone: 3G4 90min treatment cell line: Embyonic stem cell (E14)
|
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 cross-linked in 2% paraformaldehyde (EMS, 15710) for 10 min and quenched with 0.125 M glycine (final concentration). Lysis was performed in 150 mM NaCl, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.5% NP-40 (Sigma-Aldrich, I8896-50ML), 1% Triton X-100 (Sigma-Aldrich, T8787). Library preparation was performed with the NEBNext Ultra DNA Library prep kit according to the manufacturer’s instructions (NEB, E7370L)
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|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
Cell line with TetO and 3xCTCFs after 90 min of Rad21 depletion
|
Data processing |
Library strategy: 4C-seq 4C paired end datasets were processed using custom made R script provided in github repository (https://github.com/giorgettilab/Mach_et_al_chromosome_dynamics/tree/master/4C) Genome_build: mm9 Supplementary_files_format_and_content: bigwig 1D vector data and an annotation file for sample information
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|
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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 |
GPL17021 |
Series (2) |
GSE197226 |
Cohesin and CTCF control chromosomal contact dynamics in living cells [4C-seq] |
GSE197238 |
Cohesin and CTCF control chromosomal contact dynamics in living cells |
|
Relations |
BioSample |
SAMN26177244 |
SRA |
SRX14252170 |