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Quantification of cell identity from single-cell gene expression profiles.


ABSTRACT: The definition of cell identity is a central problem in biology. While single-cell RNA-seq provides a wealth of information regarding cell states, better methods are needed to map their identity, especially during developmental transitions. Here, we use repositories of cell type-specific transcriptomes to quantify identities from single-cell RNA-seq profiles, accurately classifying cells from Arabidopsis root tips and human glioblastoma tumors. We apply our approach to single cells captured from regenerating roots following tip excision. Our technique exposes a previously uncharacterized transient collapse of identity distant from the injury site, demonstrating the biological relevance of a quantitative cell identity index.

SUBMITTER: Efroni I 

PROVIDER: S-EPMC4354993 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature

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Quantification of cell identity from single-cell gene expression profiles.

Efroni Idan I   Ip Pui-Leng PL   Nawy Tal T   Mello Alison A   Birnbaum Kenneth D KD  

Genome biology 20150122


The definition of cell identity is a central problem in biology. While single-cell RNA-seq provides a wealth of information regarding cell states, better methods are needed to map their identity, especially during developmental transitions. Here, we use repositories of cell type-specific transcriptomes to quantify identities from single-cell RNA-seq profiles, accurately classifying cells from Arabidopsis root tips and human glioblastoma tumors. We apply our approach to single cells captured from  ...[more]

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