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| Status |
Public on Dec 13, 2023 |
| Title |
pEF-2-C |
| Sample type |
SRA |
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| Source name |
Porcine embryonic fibroblast
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| Organism |
Sus scrofa |
| Characteristics |
developmental stage: E30 fetal
tissue: Embryonic fibroblast
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The 1×10^6 cells were cross-linked with a final concentration of 4% formaldehyde for 30min at room temperature and followed by quenching with glycine in a final concentration of 0.25 mol/L. Mixtures were next centrifuged at 1,500×g for 10min at room temperature, and separated supernatant were added lysis buffer and incubate 15 min on ice. The mixture was then centrifuged at 5,000×g for 10 min in room temperature. The sediment was washed with 100μL 1×NEBuffer 2. The mixture was added with SDS in a final concentration of 0.1% and incubate 10min at 65°C, then added with TritonX-100 in a final concentration of 1% and incubate 15min at 37°C, thus nuclei of cells were permeabilized.
DNA was digested with 200 units of DpnII (a 4-cutter restriction enzyme) for one hour at 37°C. The restriction fragment overhangs were filled and labeled by biotinylated nucleotides and then ligated in a small volume. After crosslink reversal, DNA were purified and sonicated to fragments about 300-500 bp by applying Covaris S220 sonicator, at which point ligated fragments were pulled down with Dynabeads™ M-280 Streptavidin (Invitrogen, Cat.N: 11206D) and also were end repaired and A-tailed. Adaptors were next ligated and DNA fragments were PCR amplified using KAPA Hyper Prep Kit (Roche, Cat.N: KK8504) for 8-10 cycles. These fragments were then performed double-size selected using AMPure XP Beads (Beckman, Cat.N: A63882) in order to isolate fragments between 300 and 800bp, which were prepped for sequencing at BGISEQ-500 platform to provided 100 bp paired-end reads. Consequently, we generated a total of ~10.91-billion valid contacts of 16 Hi-C libraries (~681.95 M contacts per library) for pgEpiSCs, and a total of ~14.34-billion valid contacts of 16 Hi-C libraries (~895.96 M contacts per library) for pEFs.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
BGISEQ-500 |
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| Data processing |
Hi-C datasets were processed using a Juicer pipeline (version 1.8.9).
The high-quality Hi-C reads was aligned against the pig reference genome (Sscrofa11.1) using BWA software (version 0.7.8) with default parameters. The alignable reads were then followed duplicated read removal step provided in Juicer and remained were unique reads. Low-quality alignments (defined as MAPQ < 30) and intra-fragment reads were filtered from unique reads thus generated valid Hi-C contacts which were used for later analysis. Intra-chromosomal contract matrices were separately generated at two resolutions (100kb and 20 kb) after normalized intrinsic biases (KR algorithm) and sequencing depth (quantile algorithm) for each Hi-C library.Inter-chromosomal contact matrices were generated after normalized intrinsic biases (KR algorithm) by using Juicer tool.
Genome_build: Suscrofa.11.1
Supplementary_files_format_and_content: The .hic file is a highly compressed binary file that stores contact matrices from multiple resolutions in a clever way, allowing random access.
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| Submission date |
Mar 25, 2021 |
| Last update date |
Dec 13, 2023 |
| Contact name |
Jianyong Han |
| E-mail(s) |
[email protected]
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| Organization name |
China Agricultural University
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| Department |
State Key Laboratory of Agrobiotechnology
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| Lab |
Han lab
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| Street address |
2rd, Yuanmingyuan West Road
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| City |
Beijing |
| ZIP/Postal code |
100083 |
| Country |
China |
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| Platform ID |
GPL26285 |
| Series (2) |
| GSE168104 |
Generation and Characterization of Stable Pig Pre-gastrulation Epiblast Stem Cell Lines [HiC] |
| GSE168107 |
Generation and Characterization of Stable Pig Pre-gastrulation Epiblast Stem Cell Lines |
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| Relations |
| BioSample |
SAMN18492184 |
| SRA |
SRX10445341 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5211793_pEF-2-C.inter_30.hic |
6.2 Gb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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