|
| Status |
Public on Mar 11, 2024 |
| Title |
HiC_ESC_BPTFko_rep1 |
| 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: BPTF knock-out
|
| 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 |
SAMN35652683 |
| SRA |
SRX20607787 |
