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 | |
| State | Accepted/In press - Jan 1 2018 |
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ASJC Scopus subject areas
- General
Cite this
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
}
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 -