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

1 Citation (Scopus)

Abstract

Although we can increasingly measure transcription, chromatin, methylation, etc. at single cell resolution, most assays survey only one aspect of cellular biology. Here we describe sci-CAR, a combinatorial indexing-based co-assay that jointly profiles chromatin accessibility and mRNA in each of thousands of single cells. As a proof-of-concept, we apply sci-CAR to 4,825 cells comprising 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)
JournalScience
DOIs
StateAccepted/In press - Jan 1 2018

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

ASJC Scopus subject areas

  • General

Cite this

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

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, 01.01.2018.

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. https://doi.org/10.1126/science.aau0730(2018)
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.
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