Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments

Ning Leng; Li-Fang Chu; Chris Barry; Yuan Li; Jeea Choi; Xiaomao Li; P. Jiang; Ron M Stewart; James A Thomson; Christina Kendziorski

doi:10.1038/nmeth.3549

Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments

Ning Leng
, Li-Fang Chu
, Chris Barry
, Yuan Li
, Jeea Choi
, Xiaomao Li
, P. Jiang
, Ron M Stewart
, James A Thomson
, Christina Kendziorski

Biological, Geological, and Environmental Sciences

University of Wisconsin – Madison
Morgridge Institute for Research
University of Wisconsin School of Medicine and Public Health
University of California Santa Barbara

Research output: Contribution to journal › Article › peer-review

134 Scopus citations

Abstract

Oscillatory gene expression is fundamental to development, but technologies for monitoring expression oscillations are limited. We have developed a statistical approach called Oscope to identify and characterize the transcriptional dynamics of oscillating genes in single-cell RNA-seq data from an unsynchronized cell population. Applying Oscope to a number of data sets, we demonstrated its utility and also identified a potential artifact in the Fluidigm C1 platform.

Original language	English
Pages (from-to)	947-950
Number of pages	4
Journal	Nature Methods
Volume	12
Issue number	10
DOIs	https://doi.org/10.1038/nmeth.3549
State	Published - Sep 29 2015

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10.1038/nmeth.3549

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AU - Li, Xiaomao

AU - Jiang, P.

AU - Stewart, Ron M

AU - Thomson, James A

AU - Kendziorski, Christina

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AB - Oscillatory gene expression is fundamental to development, but technologies for monitoring expression oscillations are limited. We have developed a statistical approach called Oscope to identify and characterize the transcriptional dynamics of oscillating genes in single-cell RNA-seq data from an unsynchronized cell population. Applying Oscope to a number of data sets, we demonstrated its utility and also identified a potential artifact in the Fluidigm C1 platform.

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Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments

Abstract

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