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

doi:10.1126/science.aau0730(2018)

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

Molecular & Medical Genetics

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

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 language	English (US)
Journal	Science
DOIs	https://doi.org/10.1126/science.aau0730(2018)
State	Accepted/In press - Jan 1 2018

ASJC Scopus subject areas

General

Access to Document

10.1126/science.aau0730(2018)

Fingerprint Dive into the research topics of 'Joint profiling of chromatin accessibility and gene expression in thousands of single cells'. Together they form a unique fingerprint.

Cite this

Cao, J., Cusanovich, D. A., Ramani, V., Aghamirzaie, D., Pliner, H. A., Hill, A. J., Daza, R. M., McFaline-Figueroa, J. L., Packer, J. S., Christiansen, L., Steemers, F. J., Adey, A., Trapnell, C., & 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 journal › Article › peer-review

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.

@article{72648988d9ba4d8685d7d4e4018ac936,

title = "Joint profiling of chromatin accessibility and gene expression in thousands of single cells",

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.",

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

year = "2018",

month = jan,

day = "1",

doi = "10.1126/science.aau0730(2018)",

language = "English (US)",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science",

}

TY - JOUR

T1 - Joint profiling of chromatin accessibility and gene expression in thousands of single cells

AU - Cao, Junyue

AU - Cusanovich, Darren A.

AU - Ramani, Vijay

AU - Aghamirzaie, Delasa

AU - Pliner, Hannah A.

AU - Hill, Andrew J.

AU - Daza, Riza M.

AU - McFaline-Figueroa, Jose L.

AU - Packer, Jonathan S.

AU - Christiansen, Lena

AU - Steemers, Frank J.

AU - Adey, Andrew

AU - Trapnell, Cole

AU - Shendure, Jay

PY - 2018/1/1

Y1 - 2018/1/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85059463080&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85059463080&partnerID=8YFLogxK

U2 - 10.1126/science.aau0730(2018)

DO - 10.1126/science.aau0730(2018)

M3 - Article

AN - SCOPUS:85059463080

JO - Science

JF - Science

SN - 0036-8075

ER -