|
| Status |
Public on Jun 03, 2021 |
| Title |
E35 skeletal muscle Hi-C replicate_1 |
| Sample type |
SRA |
| |
|
| Source name |
skeletal muscle
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Luchuan pig
tissue type: longissimus dorsi muscle
age: embryonic day 35
Sex: female
chip antibody: none
restriction enzyme: DpnII (R0543S, NEB)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C experiment were conducted using DpnII, according to the protocol published by Suhas S P Rao. et al. Cell 2014 (PMID: 25497547) except for using 4% formaldehyde.
DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Suhas S P Rao. et al. Cell 2014 (PMID: 25497547).
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Reads were mapped to the pig genome (Sscrofa 11.1) by BWA (v 0.7.15).
Juicer were used HiC data processing to filter duplication, low-quality alignment read pairs (MAPQ < 30) as well as intra-fragment read pairs.
High-quality reads normalized with Knight-Ruiz [KR] algorithm and quantile algorithm to structure contact matrixes at 20 or 100 kb resolution.
Compartments A/B were identified with A-B index as as described by M Jordan Rowley. et al. Mol Cell. 2017 (PMID: 28826674).
Locations of topologically associated domains (TADs) were computed by combining directionality index (Dixon et al. Nature. 2012 [PMID: 22495300]) and insulation index (Emily Crane et al. Nature. 2017)
Genome_build: Sscrofa11.1
|
| |
|
| Submission date |
Feb 08, 2021 |
| Last update date |
Jun 03, 2021 |
| Contact name |
Renqiang Yuan |
| E-mail(s) |
yuanrq3@mail2.sysu.edu.cn
|
| Organization name |
SUN YAT-SEN UNIVERSITY
|
| Street address |
No. 135, Xingang Xi Road
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510275 |
| Country |
China |
| |
|
| Platform ID |
GPL26285 |
| Series (1) |
| GSE166346 |
Reorganization of chromatin architecture during prenatal development of porcine skeletal muscle |
|
| Relations |
| BioSample |
SAMN17833785 |
| SRA |
SRX10048351 |
