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Sample GSM2863717 Query DataSets for GSM2863717
Status Public on Nov 28, 2017
Title CTCF-ChIPSeq-Patski-Inv-Dxz4
Sample type SRA
 
Source name Patski cells
Organism Mus musculus x Mus spretus
Characteristics cell line: Patski cells
cell type: Fibroblasts derived from hybrid embryonic kidney
strain/background: BL6/spretus
genotype/variation: Inv-Dxz4
chip antibody: Anti-CTCF Antibody (Rabbit Polyclonal Antibody; Millipore 07-729)
Extracted molecule genomic DNA
Extraction protocol ChIP was performed using fixed chromatin from cell lines. DNA from ChIP pull-down chromatin fractions were de-crosslinked and purified using QIAquick PCR purification kit.
Sequencing libraries were prepared from each CTCF ChIP sample from Patski cells using the Illumina seq sample prep kit. Size selection of the library was done by gel excision and purification of DNA in the 300-600bp range. Control sequencing library was prepared from genomic DNA.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description CTCF ChIP-seq experiment in CRISPR/cas9-modified Patski cells.
Input sample: Input-DNA-Patski-Del-hinge
Data processing CTCF and input ChIP-seq paired-end reads were mapped to the BL6 genome using the NCBI build v38/mm10 reference genome assembly obtained from the UCSC Genome Browser46 using BWA-MEM (v0.7.3) in paired-end mode using default parameters.
Primary mapped valid paired reads with MAPQ>=10 were de-duplicated and used for calling CTCF peaks based on biallelic reads using MACS2. CTCF peaks were called using all reads (unsegregated) after normalization to their chromatin inputs.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bed, xls
 
Submission date Nov 22, 2017
Last update date May 15, 2019
Contact name Xinxian Deng
E-mail(s) dengx2@u.washington.edu
Organization name University of Washington
Department Laboratory Medicine and Pathology
Lab HSB C526
Street address 1959 NE Pacific St.
City Seattle
State/province WA
ZIP/Postal code 98195
Country USA
 
Platform ID GPL20213
Series (2)
GSE59779 Studies of regulation of mouse X inactivation and genes escaping XCI
GSE107286 An evaluation of the effects of CRISPR/cas9-mediated editing of the Dxz4 locus on regulation of the mouse inactive X chromosome in Patski cells [ChIP-seq]
Relations
BioSample SAMN08057760
SRA SRX3417604

Supplementary file Size Download File type/resource
GSM2863717_CTCF.peaks.patski.Inv-Dxz4.bed.gz 484.9 Kb (ftp)(http) BED
GSM2863717_CTCF.peaks.patski.Inv-Dxz4.xls.gz 1.8 Mb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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