title: Massively multiplex single-cell Hi-C.
abstract: 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.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Vijay
authors.identifier: 0000-0003-3345-5960
authors.initials: V
authors.lastname: Ramani
authors.affiliation: Department of Pathology, University of Washington, Seattle, Washington, USA.
authors.forename: Xinxian
authors.initials: X
authors.lastname: Deng
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Ruolan
authors.initials: R
authors.lastname: Qiu
authors.affiliation: Illumina Inc., Advanced Research Group, San Diego, California, USA.
authors.forename: Kevin L
authors.initials: KL
authors.lastname: Gunderson
authors.affiliation: Illumina Inc., Advanced Research Group, San Diego, California, USA.
authors.forename: Frank J
authors.initials: FJ
authors.lastname: Steemers
authors.affiliation: Department of Pathology, University of Washington, Seattle, Washington, USA.|Department of Medicine, University of Washington, Seattle, Washington, USA.
authors.forename: Christine M
authors.initials: CM
authors.lastname: Disteche
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: William S
authors.identifier: 0000-0001-7283-4715
authors.initials: WS
authors.lastname: Noble
authors.affiliation: Division of Hematology, University of Washington School of Medicine, Seattle, Washington, USA.|Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA.
authors.forename: Zhijun
authors.identifier: 0000-0002-8147-793X
authors.initials: Z
authors.lastname: Duan
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.|Howard Hughes Medical Institute, Seattle, Washington, USA.
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
mesh_terms: D002453:Cell Cycle / Q000235:genetics; D045744:Cell Line, Tumor; D002875:Chromosomes / Q000235:genetics*; D004247:DNA / Q000032:analysis / Q000235:genetics*; D015723:Gene Library; D015894:Genome, Human / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006367:HeLa Cells; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D008968:Molecular Conformation; D017422:Sequence Analysis, DNA / Q000379:methods; D059010:Single-Cell Analysis / Q000379:methods*
chemical_list: D004247:DNA