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Massively multiplex single-cell Hi-C

Vijay Ramani, Xinxian Deng, Kevin L Gunderson, Frank J Steemers, Christine M Disteche, William S Noble, Zhijun Duan, Jay Shendure
doi: https://doi.org/10.1101/065052
Vijay Ramani
1Department of Genome Sciences, University of Washington, Seattle, WA
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Xinxian Deng
2Department of Pathology, University of Washington, Seattle, WA
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Kevin L Gunderson
3Illumina Inc., Advanced Research Group, San Diego, CA
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Frank J Steemers
3Illumina Inc., Advanced Research Group, San Diego, CA
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Christine M Disteche
2Department of Pathology, University of Washington, Seattle, WA
4Department of Medicine, University of Washington, Seattle, WA
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William S Noble
1Department of Genome Sciences, University of Washington, Seattle, WA
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Zhijun Duan
5Division of Hematology, University of Washington School of Medicine, Seattle, WA
6Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA
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  • For correspondence: zjduan@uw.edu shendure@uw.edu
Jay Shendure
1Department of Genome Sciences, University of Washington, Seattle, WA
7Howard Hughes Medical Institute, Seattle, WA
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  • For correspondence: zjduan@uw.edu shendure@uw.edu
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Abstract

We present combinatorial single cell Hi-C, a novel method that leverages combinatorial cellular indexing to measure chromosome conformation in large numbers of single cells. In this proof-of-concept, we generate and sequence combinatorial single cell Hi-C libraries for two mouse and four human cell types, comprising a total of 9,316 single cells across 5 experiments. We demonstrate the utility of single-cell Hi-C data in separating different cell types, identify previously uncharacterized cell-to-cell heterogeneity in the conformational properties of mammalian chromosomes, and demonstrate that combinatorial indexing is a generalizable molecular strategy for single-cell genomics.

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Posted July 23, 2016.
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Massively multiplex single-cell Hi-C
Vijay Ramani, Xinxian Deng, Kevin L Gunderson, Frank J Steemers, Christine M Disteche, William S Noble, Zhijun Duan, Jay Shendure
bioRxiv 065052; doi: https://doi.org/10.1101/065052
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Massively multiplex single-cell Hi-C
Vijay Ramani, Xinxian Deng, Kevin L Gunderson, Frank J Steemers, Christine M Disteche, William S Noble, Zhijun Duan, Jay Shendure
bioRxiv 065052; doi: https://doi.org/10.1101/065052

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