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| Status |
Public on May 11, 2023 |
| Title |
NC_RAD.replicate_7.hic |
| Sample type |
SRA |
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| Source name |
retroperitoneal adipose
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| Organism |
Sus scrofa |
| Characteristics |
tissue: retroperitoneal adipose
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
1 g adipose tissue were pulverized, and 37% formaldehyde was added to obtain a final concentration of 4% for chromatin cross-linking. Mixture were incubated at room temperature (20–25℃) for 30 minutes, then glycine was added to obtain a final concentration of 0.25 mol/L to quench the formaldehyde. The mixture was then centrifuge at 1,500×g for 10 min at room temperature, and sediment was added the lysis buffer and homogenized. Homogenate was centrifuge at 5,000×g for adipocytes sediment. Nuclei of formaldehyde fixed adipose tissue were permeabilized and DNA was digested with 200 units of MboI (a 4-cutter restriction enzyme) for one hour at 37℃. The restriction fragment overhangs were filled and labbled 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 streptavidin beads and prepped for Illumina NovaSeq 6000 sequencing.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
whole.samples.ABindex.results.txt.gz
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| Data processing |
Contacts matrix were generated by using juicer tools.
TADs were identified using deDoc.
Compartment A/B were defined by ABindex.
Susscrofa11.1
TAD files
ABindex files
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| Submission date |
Jun 21, 2022 |
| Last update date |
May 11, 2023 |
| Contact name |
jin long |
| E-mail(s) |
longjin8806@163.com
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| Organization name |
Sichuan Agricultural University
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| Street address |
Hui ming
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| City |
Chengdu |
| ZIP/Postal code |
611130 |
| Country |
China |
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| Platform ID |
GPL26351 |
| Series (1) |
| GSE206539 |
Dynamic chromatin architecture of the porcine adipose tissues with weight gain and loss |
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| Relations |
| BioSample |
SAMN19018549 |
| SRA |
SRX11010907 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6256182_NC_RAD.replicate_7.TAD.bed.gz |
25.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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