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Sample GSM3660459 Query DataSets for GSM3660459
Status Public on May 15, 2019
Title 4C_27kb_chr1_CTCF_repl2
Sample type SRA
 
Source name 4C_27kb_chr1_CTCF
Organism Mus musculus
Characteristics cell type: embryonic stem cells (ESCs)
clone: 2.7kb teto integrations
Treatment protocol no treatment
Growth protocol Cells were cultured on gelatin-coated culture plates in Dulbecco Modified Eagle’s medium (Sigma) in the presence of 15% foetal calf serum (Eurobio Abcys), 100 µM β-mercaptoethanol, 20 U/ml leukemia inhibitory factor (Miltenyi Biotec, premium grade) in 8% CO2 at 37°C. After insertion of the rTetR-Dam vector (see below), cells were cultured in the presence of 250 µg/mL hygromycin.
Extracted molecule genomic DNA
Extraction protocol The initial steps of 4C protocol were performed as published before (Splinter et al., 2012; Methods (PMID: 22929766)).
Briefly, cells are cross-linked using 2% formaldehyde for 10min at room temperature in PBS 10%FCS and nuclei are isolated, after which chromatin is digested with DpnII and subsequently ligated. After reversal of the cross-links, the DNA is purified and treated with the second restriction enzyme Csp6I. After a second re-ligation step, the sample is purified and a 4C PCR directly on this template for mouse genome viewpoints. In order to PCR amplify the ectopic TetO viewpoint, 4C templates were treated with Cas9 in vitro. Cas9 is targeted into the TetO repeats by using a sgRNA designed in between 4C viewpoint primers.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description S19_TetO_4C_Chris_TetO_ES_27_2_Chr1_VP21
Data processing library strategy: 4C-seq
Single-end reads from each sample were mapped to the mouse genomes using the QuasR software (v 1.20.0, qAlign function, default settings).
4C signal quantification was done using qAlign (from QuasR, v 1.20.0) using as query a GRanges object containing the position of GATC sites. Library sizes are rescaled to the minimum library size
Running average of the signal was done using 21 steps
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including genomic coordinates and enrichments
 
Submission date Mar 07, 2019
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)
GSE128014 DamC reveals principles of chromatin folding in vivo without crosslinking and ligation [4C]
GSE128017 DamC reveals principles of chromatin folding in vivo without crosslinking and ligation
Relations
BioSample SAMN11083070
SRA SRX5493737

Supplementary file Size Download File type/resource
GSM3660459_filteredreverse_repl2.txt_20steps.txt.gz 35.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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