title: 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.
authors.affiliation: Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, 10003, USA. ie10@nyu.edu.
authors.forename: Idan
authors.initials: I
authors.lastname: Efroni
authors.affiliation: Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, 10003, USA. pli1@nyu.edu.
authors.forename: Pui-Leng
authors.initials: PL
authors.lastname: Ip
authors.affiliation: Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, 10003, USA. tn225@nyu.edu.
authors.forename: Tal
authors.initials: T
authors.lastname: Nawy
authors.affiliation: Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, 10003, USA. aem406@nyu.edu.
authors.forename: Alison
authors.initials: A
authors.lastname: Mello
authors.affiliation: Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, 10003, USA. ken.birnbaum@nyu.edu.
authors.forename: Kenneth D
authors.initials: KD
authors.lastname: Birnbaum
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000166:cytology / Q000235:genetics; D014408:Biomarkers, Tumor / Q000378:metabolism; D001932:Brain Neoplasms / Q000473:pathology; D045744:Cell Line, Tumor; D020869:Gene Expression Profiling; D005909:Glioblastoma / Q000473:pathology; D006801:Humans; D018519:Meristem / Q000166:cytology / Q000235:genetics; D051379:Mice; D000066450:Mouse Embryonic Stem Cells / Q000378:metabolism; D012038:Regeneration; D017423:Sequence Analysis, RNA; D059010:Single-Cell Analysis / Q000379:methods*
chemical_list: D014408:Biomarkers, Tumor