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| Status |
Public on Apr 12, 2022 |
| Title |
Hi-C data of Chicken replicate 1 |
| Sample type |
SRA |
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| Source name |
White Leghorn Embryo Fibroblasts
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| Organism |
Gallus gallus |
| Characteristics |
cell type: Fibroblasts
tissue source: Embyo
age: Embyo
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| Treatment protocol |
None
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| Growth protocol |
Most of the fibroblasts were grown in Dulbecco's Modified Eagle Medium (DMEM, 11995-065, Gibco) containing 10% Fetal Bovine Serum (FBS, 10099-141, Gibco) and 1× penicillin/streptomycin (P/S, 15140-122, Gibco), incubated at 37 °C in 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, about 20 to 25 million cells were crosslinked with 2% formaldehyde for 10 min at room temperature (20–25 °C), then used glycine to quench the formaldehyde in a final concentration of 0.25 M at room temperature for 5 min, and subsequently on ice for 15 min.
Dilution Hi-C was performed as a previous study (Lieberman-Aiden, E. et al. ). Nuclei were permeabilized by a Dounce homogenizer in the presence of cold lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630, and 1× protease inhibitor solution). DNA was digested with 400 units of HindⅢ, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume (8 mL). After reversal of cross-links, ligated DNA was purified and prepped for Illumina sequencing.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Read pair flies in fastq format were aligned to the reference genome, filtered and binned into raw and normalized 2D contact matrices using Hiclib.
TADs were identified using DomainCaller
Compartment A/B identification at 20-Kb was performed by using A-B index value which represented the comparative likelihood of a sequence interacting with A or B (100-Kb) as described previously (Rowley, M. J. et al. ). Bins at 20-Kb with positive values (more association with A at 100-Kb) were called as A compartments, while 20-Kb bins with negative values (more association with B at 100-Kb) were called as B compartments. These positive or negative values were termed as A-B index values.
Genome_build: Genome building GRCh38 of human, Mmul_8.0.1 of monkey, GRCm38 of mouse, Rnor_6.0 of rat, OryCun2.0 of rabbit, Felis_cattus_6.2 of cat, CanFam3.1 of dog, Sscrofa11.1 of pig, UMD3.1 of cow, Oar_v3.1 of sheep, GRCz10 of zebrafish, and Gallus_gallus-5.0 of chicken were used for read alignment.
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| Submission date |
Feb 25, 2021 |
| Last update date |
Apr 12, 2022 |
| Contact name |
Mengnan He |
| E-mail(s) |
hemengnan816@126.com
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| Phone |
15283521733
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| Organization name |
Sichuan Agriculture University
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| Street address |
Huimin road 211#
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| City |
Chengdu |
| ZIP/Postal code |
611130 |
| Country |
China |
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| Platform ID |
GPL24517 |
| Series (2) |
| GSE167579 |
Comparative 3D Genome Architecture in Vertebrates (Hi-C) |
| GSE167581 |
Comparative 3D Genome Architecture in Vertebrates |
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| Relations |
| BioSample |
SAMN18060236 |
| SRA |
SRX10171695 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5110941.hdf5 |
1.6 Gb |
(ftp)(http) |
HDF5 |
| GSM5110941_BLH12.ABindex.xls.gz |
600.7 Kb |
(ftp)(http) |
XLS |
| GSM5110941_Chicken.BLH12.DI.tad.bed.gz |
7.4 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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