PT - JOURNAL ARTICLE AU - Vijay Ramani AU - Xinxian Deng AU - Kevin L Gunderson AU - Frank J Steemers AU - Christine M Disteche AU - William S Noble AU - Zhijun Duan AU - Jay Shendure TI - Massively multiplex single-cell Hi-C AID - 10.1101/065052 DP - 2016 Jan 01 TA - bioRxiv PG - 065052 4099 - http://biorxiv.org/content/early/2016/07/23/065052.short 4100 - http://biorxiv.org/content/early/2016/07/23/065052.full AB - 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.