Amplification-Free Library Preparation with {{SAFE Hi}}-{{C}} Uses Ligation Products for Deep Sequencing to Improve Traditional {{Hi}}-{{C}} Analysis
Amplification-Free Library Preparation with {{SAFE Hi}}-{{C}} Uses Ligation Products for Deep Sequencing to Improve Traditional {{Hi}}-{{C}} Analysis
复制标题
使用 SAFE Hi-C 进行免扩增文库制备，使用连接产品进行深度测序，以改进传统的 Hi-C 分析
DOI：
10.1038/s42003-019-0519-y
复制
发表时间：
2019
影响因子：
5.9
通讯作者：
Hou Chunhui
中科院分区：
文献类型：
--
作者：
Niu Longjian;Shen Wei;Huang Yingzhang;He Na;Zhang Yuedong;Sun Jialei;Wan Jing;Jiang Daxin;Yang Manyun;Tse Yu Chung;Li Li;Hou Chunhui
PCR amplification of Hi-C libraries introduces unusable duplicates and results in a biased representation of chromatin interactions. We present a simplified, fast, and economically efficient Hi-C library preparation procedure, SAFE Hi-C, which generates sufficient non-amplified ligation products for deep sequencing from 30 millionDrosophilacells. Comprehensive analysis of the resulting data shows that amplification-free Hi-C preserves higher complexity of chromatin interaction and lowers sequencing depth for the same number of unique paired reads. For human cells which have a large genome, SAFE Hi-C recovers enough ligated fragments for direct high-throughput sequencing without amplification from as few as 250,000 cells. Comparison with published in situ Hi-C data from millions of human cells demonstrates that amplification introduces distance-dependent amplification bias, which results in an increased background noise level against genomic distance. With amplification bias avoided, SAFE Hi-C may produce a chromatin interaction network more faithfully reflecting the real three-dimensional genomic architecture.
