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Nat Biotechnol DOI:10.1038/nbt.2859

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.

Publication TypeJournal Article
Year of Publication2014
AuthorsTrapnell, C, Cacchiarelli, D, Grimsby, J, Pokharel, P, Li, S, Morse, M, Lennon, NJ, Livak, KJ, Mikkelsen, TS, Rinn, JL
JournalNat Biotechnol
Date Published2014 Apr
KeywordsAlgorithms, Cell Differentiation, Cells, Cultured, Gene Expression Profiling, Gene Expression Regulation, Genomics, Humans, Muscle Development, Myoblasts, Reproducibility of Results, Transcription Factors, Transcriptome

Defining the transcriptional dynamics of a temporal process such as cell differentiation is challenging owing to the high variability in gene expression between individual cells. Time-series gene expression analyses of bulk cells have difficulty distinguishing early and late phases of a transcriptional cascade or identifying rare subpopulations of cells, and single-cell proteomic methods rely on a priori knowledge of key distinguishing markers. Here we describe Monocle, an unsupervised algorithm that increases the temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points. Applied to the differentiation of primary human myoblasts, Monocle revealed switch-like changes in expression of key regulatory factors, sequential waves of gene regulation, and expression of regulators that were not known to act in differentiation. We validated some of these predicted regulators in a loss-of function screen. Monocle can in principle be used to recover single-cell gene expression kinetics from a wide array of cellular processes, including differentiation, proliferation and oncogenic transformation.


Alternate JournalNat. Biotechnol.
PubMed ID24658644
PubMed Central IDPMC4122333
Grant ListDP2 OD006670 / OD / NIH HHS / United States
P01 GM099117 / GM / NIGMS NIH HHS / United States
1DP2OD00667 / OD / NIH HHS / United States
P01GM099117 / GM / NIGMS NIH HHS / United States
P50 HG006193 / HG / NHGRI NIH HHS / United States
P50HG006193-01 / HG / NHGRI NIH HHS / United States