Massively multiplex single-cell Hi-C

Nat Methods. 2017 Mar;14(3):263-266. doi: 10.1038/nmeth.4155. Epub 2017 Jan 30.


We present single-cell combinatorial indexed Hi-C (sciHi-C), a method that applies combinatorial cellular indexing to chromosome conformation capture. In this proof of concept, we generate and sequence six sciHi-C libraries comprising a total of 10,696 single cells. We use sciHi-C data to separate cells by karyotypic and cell-cycle state differences and identify cell-to-cell heterogeneity in mammalian chromosomal conformation. Our results demonstrate that combinatorial indexing is a generalizable strategy for single-cell genomics.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Cell Cycle / genetics
  • Cell Line, Tumor
  • Chromosomes / genetics*
  • DNA / analysis
  • DNA / genetics*
  • Gene Library
  • Genome, Human / genetics*
  • Genomics / methods*
  • HeLa Cells
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • Molecular Conformation*
  • Sequence Analysis, DNA / methods
  • Single-Cell Analysis / methods*


  • DNA