Quantification of cell identity from single-cell gene expression profiles

Idan Efroni, Pui Leng Ip, Tal Nawy, Alison Mello, Kenneth Birnbaum

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number9
JournalGenome Biology
Volume16
Issue number1
DOIs
StatePublished - Jan 22 2015

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Transcriptome
gene expression
RNA
repository
tumor
cells
Meristem
root tips
Glioblastoma
Arabidopsis
transcriptome
Biological Sciences
neoplasms
index
method
Wounds and Injuries
methodology
Neoplasms

ASJC Scopus subject areas

  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Quantification of cell identity from single-cell gene expression profiles. / Efroni, Idan; Ip, Pui Leng; Nawy, Tal; Mello, Alison; Birnbaum, Kenneth.

In: Genome Biology, Vol. 16, No. 1, 9, 22.01.2015.

Research output: Contribution to journalArticle

Efroni, Idan ; Ip, Pui Leng ; Nawy, Tal ; Mello, Alison ; Birnbaum, Kenneth. / Quantification of cell identity from single-cell gene expression profiles. In: Genome Biology. 2015 ; Vol. 16, No. 1.
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