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| Status |
Public on Apr 25, 2023 |
| Title |
sheep1-GOM.HiC |
| Sample type |
SRA |
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| Source name |
greater omentum fat
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| Organism |
Ovis aries |
| Characteristics |
breed: Small-tail Han sheep
developmental stage: Adult
age: 2-year-old
tissue: greater omentum fat
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, 1 g of adipose tissue were cross-linked with a final concentration of 4% freshly prepared formaldehyde (Sigma Aldrich, Louis, MO, USA) for 30 mins at room temperature, followed by quenching with glycine (Amresco, Solon, OH, USA) at a final concentration of 0.25 mol/L. After centrifuging the mixture at 1500 × g for 10 mins at room temperature, the upper layer containing adipocytes were added to 1 mL lysis buffer (9.1 μL 1 M NaCl, 9.1 μL 1 M Tris-HCl [pH 8.0] [Invitrogen, Carlsbad, CA, USA], 18.2 μL 10% CA-630 [Sigma Aldrich, Louis, MO, USA], 50 μL protease inhibitors [Sigma Aldrich, Louis, MO, USA], and 913.6 μL nuclease-free water [Ambion, Carlsbad, CA, USA]) and homogenized with a Dunce homogenizer. After centrifuging the homogenate at 5000×g, cell nuclei were collected. The pellet was washed twice with 500 μL 1× NEBuffer 2 (NEB, Ipswich, MA, USA), followed by centrifugation at 5000 rpm for 5 mins. Next, the pellet was resuspended in 100 µL 1× NEBuffer 2, and we added SDS (Amresco, Solon, OH, USA) to a final concentration of 0.1%. After incubation at 65 °C for 10 mins, we added Triton X-100 (Sigma Aldrich, Louis, MO, USA) to a final concentration of 1%, and incubated for 15 mins at 37 °C. Nuclei were permeabilized, and DNA was digested with 200 units of MboI enzyme (NEB, Ipswich, MA, USA) at 37 °C for 1 h, 65 °C for 20 mins and 25 °C for 5 mins. We then added biotin-14-dATP, dCTP, dGTP, dTTP and Klenow fragment (NEB, Ipswich, MA, USA), and incubated the mixture at 37 °C for 45 mins. The DNA fragments were then ligated by T4 DNA ligase (Enzymatics, Beverly, MA, USA), incubated at 20 °C for 30 mins. After centrifugation at 5000 rpm for 5 mins, the pellet was resuspended in 20 µL 10X T4 DNA ligase buffer, 90 µL nuclease-free water, and 20 µL SDS and 50 µL Proteinase K (20 mg/ml) (Tiangen, Beijing, China) were added. After incubation at 55 °C for 30 min to digest proteins, the DNA were extracted and dissolved in 20 µL of 5 M NaCl, and the mixture was incubated sequentially at 65 °C for 90 mins and at 25 °C for 5 mins. The DNA were then purified by AMPure XP Beads (Beckman Coulter, Brea, CA, USA). Then, T4 DNA polymerase (Enzymatics, Beverly, MA, USA) was used to remove nonligated biotinylated DNA for 2 h at 12 °C. The DNA was then sonicated into 300-500 bp fragments using a Covaris S220 sonicator. The DNA fragments with biotin were pulldown by M280 beads (Invitrogen, Carlsbad, CA, USA).
Next, we performed end repair, A-tailing, adapter ligation, postligation cleanup and PCR amplification (8-10 cycles) using the KAPA Hyper Prep Kit (Roche, Pleasanton, CA, USA). DNAs between 300 and 800 bp in size were then isolated using AMPure XP Beads, and the libraries were sequenced using Illumina NovaSeq 6000 (paired-end sequencing with 150 bp read length).
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Contacts matrix were generated by using Juicer pipeline.
Gene-level expression was estimated as transcripts per million (TPM) using the high-speed transcript quantification tool Kallisto (version 0.43.0).
Tpm and counts matrixs were generated using R vresion 3.6.1.
TADs were identified using Insulation Score.
Compartment A/B were defined by A-B index.
Assembly: Susscrofa11.1
Supplementary files format and content: Binned raw and normalized 2D contact matrices text files
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Genes expression level (TPM) and counts text file
Supplementary files format and content: TAD files
Supplementary files format and content: ABindex files
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| Submission date |
Apr 01, 2022 |
| Last update date |
Apr 25, 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 |
GPL27721 |
| Series (1) |
| GSE199968 |
Comparative 3D Genome Architectures of Adipose Tissues Provide Insight into Human-specific Regulation of Metabolic Homeostasis |
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| Relations |
| BioSample |
SAMN26748020 |
| SRA |
SRX14491720 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5997661_sheep1-GOM.20k.100k.inter_30.hic |
266.2 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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