Iteratively improving Hi-C experiments one step at a time

• Published in: Methods (San Diego, Calif.) Vol. 142; pp. 47 - 58
• Main Authors: Golloshi, Rosela, Sanders, Jacob T., McCord, Rachel Patton
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.06.2018
• Subjects: 3D genome structure; biomarkers; cell division; chromatin; Chromatin - chemistry; Chromatin - genetics; Chromosome conformation capture; Chromosome Mapping - instrumentation; Chromosome Mapping - methods; Cross-Linking Reagents - chemistry; data quality; Datasets as Topic; DNA; DNA - chemistry; DNA damage; DNA replication; DNA Restriction Enzymes - chemistry; Formaldehyde - chemistry; gene expression; Gene Library; genome; genomics; Hep G2 Cells; Hi-C; High throughput sequencing; High-Throughput Nucleotide Sequencing - instrumentation; High-Throughput Nucleotide Sequencing - methods; Humans; protocols; Sequence Analysis, DNA - instrumentation; Sequence Analysis, DNA - methods; Chromosome conformation capture; High throughput sequencing; Hi-C; 3D genome structure

•Variability in Hi-C libraries can arise from early steps of cell preparation.•Hi-C 2.0 changes also benefit libraries generated by 6-cutter enzymes.•Artificial molecule fusions can arise during end repair and PCR, increasing noise.•Common causes of Hi-C DNA loss identified for future optimization....