Systematic evaluation of ligation conditions in chromatin conformation capture experiments, second batch
Release date:
2024-08-20
Description:
Chromosome conformation capture (3C) and related assays are popular technologies for mapping the three-dimensional chromatin organizations. Ligation between interacted chromatin fragments by formaldehyde is the first and one of the most important steps in such protocols. There are two vital parameters in the ligation step--the ligation temperature and concentration of the formaldehyde. Unfortunately, there are several commonly used, different, combinations of these parameters and there was no systematic evaluation of the effects of them to the resulted chromatin conformation maps. Here we applied different combinations of ligation temperature and concentration of the formaldehyde to high-throughput chromatin conformation capture (Hi-C), and evaluated the influences of ligation conditions to the analysis of spatial chromatin organization in every level, from the overall contact frequencies to the A/B compartments, TADs and loops. This is the 2nd batch of sequencing data, with both K562 and GM12878.
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Individuals & samples
Files
Submitter: Zhang Zhihua / zhangzhihua@big.ac.cn
Organization: Beijing Institute of Genomics, Chinese Academy of Sciences
Submission date: 2023-12-01
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HRA006154.xlsx