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| Status |
Public on Nov 28, 2017 |
| Title |
insituDNaseHiC-WG-Patski-WT |
| Sample type |
SRA |
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| Source name |
Patski cells
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| 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
experiment: in situ DNase Hi-C
library: whole-genome
replicate: 3
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
in situ DNase Hi-C: Cells are cross-linked with formaldehyde; chromatin is then randomly fragmented by DNase I. The resulting chromatin fragments are end-repaired and dA-tailed, then marked with a biotinylated internal adaptor; and proximity ligation is carried out inside individual nuclei to favor ligation events between the cross-linked DNA fragments. The resulting DNA sample contains ligation products consisting of chimeric DNA fragments that were originally in close spatial proximity in the nucleus, marked with biotin at the junction. A whole-genome chromatin interaction library is created by shearing the DNA and selecting the biotin-containing fragments with streptavidin magnetic beads. After linear library amplification, a DNase Hi-C library is generated and can be sequenced to identify whole-genome chromatin contacts.
in situ DNase Hi-C.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
in situ DNase Hi-C experiment in wild-type Patski cells.
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| Data processing |
Library strategy: DNase Hi-C
For each in situ DNase Hi-C library, we mapped each end of the paired-end reads separately to the BL6 genome using the NCBI build v38/mm10 reference genome assembly obtained from the UCSC Genome Browser and a pseudo-spretus genome using BWA-MEM (v0.7.3) in single-end mode using default parameters. A pseudo-spretus genome was assembled by substituting available SNPs (from Sanger Institute, SNP database 2014/10/27 v4) into the BL6 reference genome.
We retained only primary reads with MAPQ ≥30 for further analysis. Using heterozygous SNPs between the BL6 genome and the pseudo-spretus genome that were validated for our particular Patski cell line, we segregated all high-quality uniquely mapped reads (MAPQ ≥30).
In order to maximize the number of reads assigned to either the BL6 Xi or the spretus Xa, we required that only one end of the read be specifically mapped to one mouse species, while the other end was allowed to be ambiguously mapped. Each end of each read pair was assigned to one of three categories: (1) BL6-SNP reads containing only BL6-specific SNP(s); (2) spretus-SNP reads containing only spretus-specific SNP(s); (3) ambiguous reads that did not contain valid SNPs or that contained valid SNPs from both alleles. We refer to both BL6-SNP reads and spretus-SNP reads as “allele-specific reads”, and reads that do not contain valid SNPs as “allele-uncertain reads”. Reads were paired with their corresponding mates, and those read pairs with at least one end being allele-specific were retained for subsequent allele-specific analysis.
To eliminate the bias due to the PCR duplication step, we removed redundant paired-end reads defined as those pairs where both ends were mapped to identical locations in the same genome assembly. This resulted in a set of valid read pairs representing DNA-DNA interactions.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: txt files, containing uniquely mapped and non-redundant read pairs. The files are tab-delimited. The columns are #1 read identifier, #2 strand of the 1st end, #3 mapped chr of the 1st end, #4 mapped coordinate of the 1st end, #5 allele of 1st read (ref: BL6; alt: spretus; both-ref; allele-uncertain reads), #6 sequence of 1st end, #7 strand of the 2nd end, #8 mapped chr of the 2nd end, #9 mapped coordinate of the 2nd end, #10 allele of 2nd read (ref: BL6; alt: spretus; both-ref; allele-uncertain reads), #11 sequence of 2nd end.
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| Submission date |
Nov 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Xinxian Deng |
| E-mail(s) |
dengx2@u.washington.edu
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| Organization name |
University of Washington
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| Department |
Laboratory Medicine and Pathology
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| Lab |
HSB C526
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| Street address |
1959 NE Pacific St.
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
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| Platform ID |
GPL20213 |
| Series (2) |
| GSE59779 |
Studies of regulation of mouse X inactivation and genes escaping XCI |
| GSE107282 |
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 [DNase HiC] |
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| Relations |
| BioSample |
SAMN08057594 |
| SRA |
SRX3417521 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2863686_insituDNaseHiC.WG.patski.WT.cleanedPairs.gz.txt.gz |
24.7 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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