|
| Status |
Public on Nov 28, 2017 |
| Title |
Input-DNA-Patski-Del-hinge |
| 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: Del-hinge
chip antibody: none
|
| 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.
|
| 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) |
[email protected]
|
| 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 |
SAMN08057761 |
| SRA |
SRX3417607 |
