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Sample GSM5911335 Query DataSets for GSM5911335
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)
 
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
 
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

Supplementary file Size Download File type/resource
GSM5911335_3xCTCF_3G4_90min.bedGraph.bw 47.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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