Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

Darren A. Cusanovich, Riza Daza, Andrew Adey, Hannah A. Pliner, Lena Christiansen, Kevin L. Gunderson, Frank J. Steemers, Cole Trapnell, Jay Shendure

Research output: Contribution to journalArticle

247 Citations (Scopus)

Abstract

Technical advances have enabled the collection of genome and transcriptome data sets with single-cell resolution. However, single-cell characterization of the epigenome has remained challenging. Furthermore, because cells must be physically separated before biochemical processing, conventional single-cell preparatory methods scale linearly. We applied combinatorial cellular indexing to measure chromatin accessibility in thousands of single cells per assay, circumventing the need for compartmentalization of individual cells. We report chromatin accessibility profiles from more than 15,000 single cells and use these data to cluster cells on the basis of chromatin accessibility landscapes. We identify modules of coordinately regulated chromatin accessibility at the level of single cells both between and within cell types, with a scalable method that may accelerate progress toward a human cell atlas.

Original languageEnglish (US)
Pages (from-to)910-914
Number of pages5
JournalScience
Volume348
Issue number6237
DOIs
StatePublished - May 22 2015

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Chromatin
Atlases
Transcriptome
Genome

ASJC Scopus subject areas

  • General
  • Medicine(all)

Cite this

Cusanovich, D. A., Daza, R., Adey, A., Pliner, H. A., Christiansen, L., Gunderson, K. L., ... Shendure, J. (2015). Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science, 348(6237), 910-914. https://doi.org/10.1126/science.aab1601

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. / Cusanovich, Darren A.; Daza, Riza; Adey, Andrew; Pliner, Hannah A.; Christiansen, Lena; Gunderson, Kevin L.; Steemers, Frank J.; Trapnell, Cole; Shendure, Jay.

In: Science, Vol. 348, No. 6237, 22.05.2015, p. 910-914.

Research output: Contribution to journalArticle

Cusanovich, DA, Daza, R, Adey, A, Pliner, HA, Christiansen, L, Gunderson, KL, Steemers, FJ, Trapnell, C & Shendure, J 2015, 'Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing', Science, vol. 348, no. 6237, pp. 910-914. https://doi.org/10.1126/science.aab1601
Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL et al. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science. 2015 May 22;348(6237):910-914. https://doi.org/10.1126/science.aab1601
Cusanovich, Darren A. ; Daza, Riza ; Adey, Andrew ; Pliner, Hannah A. ; Christiansen, Lena ; Gunderson, Kevin L. ; Steemers, Frank J. ; Trapnell, Cole ; Shendure, Jay. / Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. In: Science. 2015 ; Vol. 348, No. 6237. pp. 910-914.
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