 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 15, 2022 |
| Title |
2y_HiC_replicate_1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Bama pig
tissue type: Developmental stage
age: 2-years-old
Sex: female
restriction enzyme: DpnII
|
| Treatment protocol |
Six two-years-old female pigs were fed with a high fat diet (15.12 MJ·kg-1 metabolizable energy, 11.26% crude protein, 6.8% fat and 5% lysine) for 22 weeks, compared with the pigs of two-years-old fed with well-characterized normal diet for 22 weeks.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Livers tissue was homogenized with liquid nitrogen then fixed with 4% formaldehyde solution and incubated at room temperature for 30 min. Glycine were added to a final concentration of 0.2 M to quench the fixing reaction, and incubated at room temperature for 5 min then centrifuge for 10 min at 1,000 g and 4˚C. Discarded supernatants and cells were lysed with 1M Tris-HCl, 1M NaCl, 10% CA-630 and protease inhibitors on ice for 15 min. Cell nucleus were washed twice and were permeabilized at 65˚C for 10 min with 1% SDS to a final concentration of 0.1%. To quench the SDS, added 10% TritonX-100 (0.1% final concentration) and incubated at 37˚C for 15 min. Then 200 U DpnII (a 4-cutter restriction enzyme) was added and digested chromatin at 37˚C for 15 min, 65˚C for 20 min and 25˚C for 5 min. The restriction fragment overhangs were filled and labelled by biotinylated nucleotides, then ligated in a small volume.
After crosslink reversal, ligated DNA was purified and sheared to a length of 300–500 bp, at which point ligation junctions were pulled down with magnetic beads and prepared for BGISEQ-500 sequencing.
|
| |
|
| 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 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)
Assembly: Sscrofa11.1
Supplementary files format and content: 20 and 100 kb matrixes, hic file
Supplementary files format and content: A-B index, txt file
Supplementary files format and content: locations of TAD for each sample, merged replicates, and consensus TAD,txt file
Supplementary files format and content: D-score, txt file
|
| |
|
| Submission date |
Mar 11, 2022 |
| Last update date |
Mar 17, 2022 |
| Contact name |
Jing Li |
| E-mail(s) |
lijing-jane@foxmail.com
|
| Phone |
+8615882474902
|
| Organization name |
Sichuan Agricultural University
|
| Department |
College of Animal Science and Technology
|
| Street address |
No. 211 Huimin Road, Wenjiang District
|
| City |
Chengdu |
| State/province |
China |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL26285 |
| Series (1) |
| GSE176387 |
Three-dimensional geome study of procine livers during development and metabolic adaptation |
|
| Relations |
| BioSample |
SAMN18317858 |
| SRA |
SRX10588964 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5946419_2y_1.TAD.txt.gz |
23.0 Kb |
(ftp)(http) |
TXT |
| GSM5946419_2y_HiC_1.20k.100k.inter_30.hic |
500.4 Mb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
