Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments (original) (raw)

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Acknowledgements

This work was supported by US National Institutes of Health grants GM102756, 4UH3TR000506 and 5U01HL099773, the Charlotte Geyer Foundation and the Morgridge Institute for Research. N.L. was supported by the Shapiro Fellowship. C.B. was supported by the Canadian Institutes of Health Research Banting Postdoctoral Fellowship. We thank M. Probasco and N. Propson for their assistance in sorting cells by FACS and J. Bolin, A. Elwell and B.K. Nguyen for the preparation and sequencing of the RNA-seq samples. We thank A. Gitter, K. Korthauer and R. Bacher for comments that helped improve the manuscript.

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Author notes

  1. Ning Leng and Li-Fang Chu: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Statistics, University of Wisconsin–Madison, Madison, Wisconsin, USA
    Ning Leng, Yuan Li, Jeea Choi & Xiaomao Li
  2. Morgridge Institute for Research, Madison, Wisconsin, USA
    Ning Leng, Li-Fang Chu, Chris Barry, Peng Jiang, Ron M Stewart & James A Thomson
  3. Department of Cell and Regenerative Biology, University of Wisconsin–Madison, Madison, Wisconsin, USA
    James A Thomson
  4. Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, USA
    James A Thomson
  5. Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, USA
    Christina Kendziorski

Authors

  1. Ning Leng
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  2. Li-Fang Chu
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  3. Chris Barry
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  4. Yuan Li
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  5. Jeea Choi
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  6. Xiaomao Li
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  7. Peng Jiang
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  8. Ron M Stewart
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  9. James A Thomson
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  10. Christina Kendziorski
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Contributions

N.L., L.-F.C., R.M.S., J.A.T. and C.K. designed research, analyzed data and wrote the manuscript; C.B. generated the H1-FUCCI cell line; Y.L., J.C. and X.L. contributed to the simulation studies; and P.J. performed RNA-seq read mapping, quantification and quality control.

Corresponding author

Correspondence toChristina Kendziorski.

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Competing interests

J.A.T. is a founder, stockholder, consultant and board member of Cellular Dynamics International (CDI).

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Leng, N., Chu, LF., Barry, C. et al. Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments.Nat Methods 12, 947–950 (2015). https://doi.org/10.1038/nmeth.3549

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