Joint profiling of chromatin accessibility and gene expression in thousands of single cells

Junyue Cao, Darren A. Cusanovich, Vijay Ramani, Delasa Aghamirzaie, Hannah A. Pliner, Andrew J. Hill, Riza M. Daza, Jose L. McFaline-Figueroa, Jonathan S. Packer, Lena Christiansen, Frank J. Steemers, Andrew Adey, Cole Trapnell, Jay Shendure

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

Although we can increasingly measure transcription, chromatin, methylation, and other aspects of molecular biology at single-cell resolution, most assays survey only one aspect of cellular biology. Here we describe sci-CAR, a combinatorial indexing-based coassay that jointly profiles chromatin accessibility and mRNA (CAR) in each of thousands of single cells. As a proof of concept, we apply sci-CAR to 4825 cells, including a time series of dexamethasone treatment, as well as to 11,296 cells from the adult mouse kidney. With the resulting data, we compare the pseudotemporal dynamics of chromatin accessibility and gene expression, reconstruct the chromatin accessibility profiles of cell types defined by RNA profiles, and link cis-regulatory sites to their target genes on the basis of the covariance of chromatin accessibility and transcription across large numbers of single cells.

Original languageEnglish (US)
Pages (from-to)1380-1385
Number of pages6
JournalScience
Volume361
Issue number6409
DOIs
StatePublished - Sep 28 2018

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Chromatin
Joints
Gene Expression
Messenger RNA
Methylation
Dexamethasone
Cell Biology
Molecular Biology
Cell Count
RNA
Kidney
Genes

ASJC Scopus subject areas

  • General

Cite this

Cao, J., Cusanovich, D. A., Ramani, V., Aghamirzaie, D., Pliner, H. A., Hill, A. J., ... Shendure, J. (2018). Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science, 361(6409), 1380-1385. https://doi.org/10.1126/science.aau0730

Joint profiling of chromatin accessibility and gene expression in thousands of single cells. / Cao, Junyue; Cusanovich, Darren A.; Ramani, Vijay; Aghamirzaie, Delasa; Pliner, Hannah A.; Hill, Andrew J.; Daza, Riza M.; McFaline-Figueroa, Jose L.; Packer, Jonathan S.; Christiansen, Lena; Steemers, Frank J.; Adey, Andrew; Trapnell, Cole; Shendure, Jay.

In: Science, Vol. 361, No. 6409, 28.09.2018, p. 1380-1385.

Research output: Contribution to journalArticle

Cao, J, Cusanovich, DA, Ramani, V, Aghamirzaie, D, Pliner, HA, Hill, AJ, Daza, RM, McFaline-Figueroa, JL, Packer, JS, Christiansen, L, Steemers, FJ, Adey, A, Trapnell, C & Shendure, J 2018, 'Joint profiling of chromatin accessibility and gene expression in thousands of single cells', Science, vol. 361, no. 6409, pp. 1380-1385. https://doi.org/10.1126/science.aau0730
Cao J, Cusanovich DA, Ramani V, Aghamirzaie D, Pliner HA, Hill AJ et al. Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science. 2018 Sep 28;361(6409):1380-1385. https://doi.org/10.1126/science.aau0730
Cao, Junyue ; Cusanovich, Darren A. ; Ramani, Vijay ; Aghamirzaie, Delasa ; Pliner, Hannah A. ; Hill, Andrew J. ; Daza, Riza M. ; McFaline-Figueroa, Jose L. ; Packer, Jonathan S. ; Christiansen, Lena ; Steemers, Frank J. ; Adey, Andrew ; Trapnell, Cole ; Shendure, Jay. / Joint profiling of chromatin accessibility and gene expression in thousands of single cells. In: Science. 2018 ; Vol. 361, No. 6409. pp. 1380-1385.
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