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Sample GSM7593323

Query DataSets for GSM7593323

Status

Public on Dec 31, 2023

Title

Hi-C_pig_spleen_r2

Sample type

SRA

Source name

spleen

Organism

Sus scrofa

Characteristics

tissue: spleen

Extracted molecule

genomic DNA

Extraction protocol

Hi-C experiments were performed following previous study (Lieberman-Aiden et al., 2009) with slight modifications. In brief, following cross-linking with 1% formaldehyde and nuclei extraction, the chromatin was digested with Dpn Ⅱ and labeled with biotinylated residue after the 5' overhangs were filled. Blunt-end ligation of crosslinked DNA fragments was performed to obtain circular molecules, and then the DNA product was purified and sonicated into DNA fragments. Hi-C library was constructed by capturing the labeled target DNA fragments with biotin labeling precipitation technique followed by size selection. Finally, the obtained Hi-C library was sequenced by BGI company as 150 bp paired-end reads on DNBSEQ platform.

Library strategy

Hi-C

Library source

genomic

Library selection

other

Instrument model

DNBSEQ-G400

Data processing

The clean Hi-C reads were iteratively mapped to the pig genome by the HiC-Pro v3.1.0 (Servant et al., 2015). We pooled the valid pairs of the two replicates together for further analysis.
The TAD structure (insulation/boundaries) was defined with Arrowhead by juicer tools v1.6 (Durand et al., 2016b).
Loops of Hi-C data were analyzed by HiCCUPS (Rao et al., 2014) with minor modifications. The resolution parameter was set as “-r 5000,10000,25000 --ignore_sparsity”.
Assembly: Sscrofa11
Supplementary files format and content: hic file for the interaction matrix
Supplementary files format and content: BED file for the identified TADs
Supplementary files format and content: BED file for the identified loops

Submission date

Jul 11, 2023

Last update date

Dec 31, 2023

Contact name

yu zhuo li

E-mail(s)

MX120210971@stu.yzu.edu.cn

Phone

15066340531

Organization name

Yangzhou University