|
| Status |
Public on Nov 28, 2017 |
| Title |
ATACseq-Patski-WT |
| Sample type |
SRA |
| |
|
| Source name |
Patski cells
|
| Organism |
Mus musculus x Mus spretus |
| Characteristics |
cell line: Patski
cell type: Fibroblasts derived from hybrid embryonic kidney
strain/background: BL6/spretus
genotype/variation: wild-type
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was done on WT, Del-hinge, Inv-Dxz4 and 2-4-clone Patski cells using a published method.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ATAC-seq experiment in wild-type Patski cells.
|
| Data processing |
ATAC-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 ATAC peaks based on biallelic reads using MACS2. ATAC peaks were called using all reads (unsegregated).
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 |
| GSE107290 |
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 [ATAC-seq] |
|
| Relations |
| BioSample |
SAMN08092868 |
| SRA |
SRX3418102 |
