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Sample GSM7461657 Query DataSets for GSM7461657
Status Public on Mar 11, 2024
Title HiC_ESC_wt_rep2
Sample type SRA
 
Source name embryonic stem cells
Organism Mus musculus
Characteristics tissue: embryonic stem cells
cell line: 129S6/SvEvTac
cell type: embryonic stem cells
genotype: wild-type
Extracted molecule genomic DNA
Extraction protocol DNA was purified using AMPure XP beads
Sequencing libraries were prepared using the NEBNext Ultra Library Preparation Kit (NEB) with 12 PCR amplification cycles for Ips and 5 PCR amplification cycles for inputs.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. Hi-C data was processed using the distiller-nf pipeline (https://github.com/open2c/distiller-nf ). Briefly, reads were mapped to mm10 using BWA (ver. 0.7.17) with default parameters "bwa mem -SP5M ".
Hi-C pairs contacts were extracted from mapped files and processed using pairtools (10.5281/zenodo.5214125), specifically with the parse (with --add-columns mapq --walks-policy all additional arguments), sort and dedup (with max_mismatch_bp: 1 setting).
Deduplicated pairs were then filtered to retain pairs with both sides mapping with high confidence (mapq>=30) and converted to cooler format using cooler ver. 0.9.0 using the ‘cload pairs’ function with default parameters. Matrices were then zoomified to produce multiresolution cooler (.mcool) files, and they were balanced with the –cis-only flag.
Assembly: mm10
Supplementary files format and content: Contact matrix in multiple cool format.
 
Submission date Jun 06, 2023
Last update date Mar 11, 2024
Contact name Dirk Schuebeler
Organization name Friedrich Miescher Institute for Biomedical Research
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platform ID GPL19057
Series (2)
GSE234292 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [Hi-C]
GSE234295 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF
Relations
BioSample SAMN35652684
SRA SRX20607784

Supplementary file Size Download File type/resource
GSM7461657_HiC_wt_rep2.mcool 819.4 Mb (ftp)(http) MCOOL
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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