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RNA velocity and protein acceleration from single-cell multiomics experiments

View ORCID ProfileGennady Gorin, View ORCID ProfileValentine Svensson, View ORCID ProfileLior Pachter
doi: https://doi.org/10.1101/658401
Gennady Gorin
1Division of Chemistry and Chemical Engineering, California Institute of Technology
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Valentine Svensson
2Division of Biology and Biological Engineering & Department of Computing and Mathematical Sciences, California Institute of Technology
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  • For correspondence: vale@caltech.edu lpachter@caltech.edu
Lior Pachter
2Division of Biology and Biological Engineering & Department of Computing and Mathematical Sciences, California Institute of Technology
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  • For correspondence: vale@caltech.edu lpachter@caltech.edu
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Abstract

The simultaneous quantification of protein and RNA makes possible the inference of past, present and future cell states from single experimental snapshots. To enable such temporal analysis from multimodal single-cell experiments, we introduce an extension of the RNA velocity method that leverages estimates of unprocessed transcript and protein abundances to extrapolate cell states. We apply the model to four datasets and demonstrate consistency among landscapes and phase portraits.

Footnotes

  • Updated link to code to https://github.com/pachterlab/GSP_2019. Revised equations in SI; fixed error in protein ODE. Revised SI figure captions.

  • https://github.com/pachterlab/GSP_2019

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 14, 2019.
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RNA velocity and protein acceleration from single-cell multiomics experiments
Gennady Gorin, Valentine Svensson, Lior Pachter
bioRxiv 658401; doi: https://doi.org/10.1101/658401
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RNA velocity and protein acceleration from single-cell multiomics experiments
Gennady Gorin, Valentine Svensson, Lior Pachter
bioRxiv 658401; doi: https://doi.org/10.1101/658401

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