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| Status |
Public on Mar 15, 2022 |
| Title |
0d_HiC_replicate_4 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Sus scrofa |
| Characteristics |
breed: Bama pig
tissue: Liver
condition: Developmental stage
age: the birth day
Sex: female
chip antibody: n/a
restriction enzyme: DpnII
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| 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.
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| 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 90 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.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
0d_4
all.samples.abindex.txt
0d.merged.replicates.tad.txt
developmental.consensus.TAD.txt
developmental.Dscore.txt
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| 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)
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: 20 and 100 kb matrixes, hic file
A-B index, txt file
locations of TAD for each sample, merged replicates, and consensus TAD,txt file
D-score, txt file
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| Submission date |
Jun 08, 2021 |
| Last update date |
Mar 17, 2022 |
| Contact name |
Jing Li |
| E-mail(s) |
lijing-jane@foxmail.com
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| Phone |
+8615882474902
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| Organization name |
Sichuan Agricultural University
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| Department |
College of Animal Science and Technology
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| Street address |
No. 211 Huimin Road, Wenjiang District
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| City |
Chengdu |
| State/province |
China |
| ZIP/Postal code |
611130 |
| Country |
China |
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| Platform ID |
GPL22475 |
| Series (1) |
| GSE176387 |
Three-dimensional geome study of procine livers during development and metabolic adaptation |
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| Relations |
| BioSample |
SAMN18317843 |
| SRA |
SRX10994540 |
| SRA |
SRX10994541 |
| SRA |
SRX10994542 |
| SRA |
SRX10994543 |
| SRA |
SRX10994544 |
| SRA |
SRX10994545 |
| SRA |
SRX10994546 |
| SRA |
SRX10994547 |
| SRA |
SRX10994548 |
| SRA |
SRX10994549 |
| SRA |
SRX10994550 |
| SRA |
SRX10994551 |
| SRA |
SRX10994552 |
| SRA |
SRX10994553 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5363628_0d_4.TAD.txt.gz |
21.9 Kb |
(ftp)(http) |
TXT |
| GSM5363628_0d_HiC_4.20k.100k.inter_30.hic |
952.6 Mb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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