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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 20, 2021 |
| Title |
Hi-C data of Cat sequenced by NovaSeq-6000 |
| Sample type |
SRA |
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| Source name |
Adipose tissue
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| Organism |
Felis catus |
| Characteristics |
breed: A native breed of cat from Chengdu city
tissue: Back fat
age: 2-year-old
developmental stage: Adult
Sex: female
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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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| Data processing |
Basecalls performed using CASAVA version 1.4
Read pair flies in fastq format were aligned to the reference genome, filtered and binned into raw and normalized 2D contact matrices using Juicer
TADs were identified using DomainCaller
Genome_build: Rnor_6.0, OryCun2.0, Sscrofa11.1, Oar_v3.1, Felis_catus_6.2 and CanFam3.1
Supplementary_files_format_and_content: valid read pairs text files
Supplementary_files_format_and_content: binned raw and normalized 2D contact matrices text files
Supplementary_files_format_and_content: TAD text files
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| Submission date |
Nov 25, 2020 |
| Last update date |
Apr 20, 2021 |
| 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 |
GPL28702 |
| Series (2) |
| GSE162140 |
A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription [non-human Hi-C] |
| GSE162148 |
A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription |
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| Relations |
| BioSample |
SAMN15870124 |
| SRA |
SRX9002158 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4942854_cat-3BF.hic |
396.2 Mb |
(ftp)(http) |
HIC |
| GSM4942854_cat-3BF.valipairs.txt.gz |
2.5 Gb |
(ftp)(http) |
TXT |
| GSM4942854_cat-3BF_TAD.txt.gz |
13.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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