%0 Journal Article %A Longjian Niu %A Wei Shen %A Yingzhang Huang %A Na He %A Yuedong Zhang %A Jialei Sun %A Jing Wan %A Daxin Jiang %A Manyun Yang %A Yu Chung Tse %A Li Li %A Chunhui Hou %T Amplification-free Library Preparation Improves Quality of Hi-C Analysis %D 2019 %R 10.1101/562280 %J bioRxiv %P 562280 %X 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 that generates sufficient non-amplified ligation products for deep sequencing from 30 million Drosophila cells. Comprehensive analysis of the resulting data indicates that amplification-free Hi-C preserves higher complexity of chromatin interaction and lowers sequencing depth dramatically for the same number of unique paired reads. For human cells which has a large genome, this method recovers an amount of ligated fragments enough for direct high-throughput sequencing without amplification on as low as 250 thousand of cells. Comparison with published in situ Hi-C on millions of human cells reveals that amplification introduces distance-dependent amplification bias, which results in increasing background noise level against genomic distance. With amplification bias avoided, our method may produce a chromatin interaction network more faithfully reflecting the real three-dimensional genomic architecture. %U https://www.biorxiv.org/content/biorxiv/early/2019/02/27/562280.full.pdf