Amplification-free library preparation with SAFE Hi-C uses ligation products for deep sequencing to improve traditional Hi-C analysis.

ABSTRACT: 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 million Drosophila cells. 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

SUBMITTER: Niu L 

PROVIDER: S-EPMC6642088 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature