Brief Communication

Alignment of single-cell trajectories to compare cellular expression dynamics

  • Nature Methods volume 15, pages 267270 (2018)
  • doi:10.1038/nmeth.4628
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Abstract

Single-cell RNA sequencing and high-dimensional cytometry can be used to generate detailed trajectories of dynamic biological processes such as differentiation or development. Here we present cellAlign, a quantitative framework for comparing expression dynamics within and between single-cell trajectories. By applying cellAlign to mouse and human embryonic developmental trajectories, we systematically delineate differences in the temporal regulation of gene expression programs that would otherwise be masked.

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Acknowledgements

This study was supported by the Israel Science Foundation (ISF) grants 1365/12 and the Applebaum Foundation. We thank Y. Ofran, M. Drukker, N. Kaplan, K. Brennand, and members of the Shen-Orr lab for fruitful discussions, and D. Alpert for assistance in algorithmic design and technical support.

Author information

Affiliations

  1. Faculty of Medicine, Technion – Israel Institute of Technology, Haifa, Israel.

    • Ayelet Alpert
    • , Lindsay S Moore
    • , Tania Dubovik
    •  & Shai S Shen-Orr

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Contributions

A.A., L.S.M. and S.S.S.-O. designed the algorithm and simulations; A.A. and L.S.M. implemented the algorithm and analyzed data; T.D. generated and helped analyze mouse B cell CyTOF data; and all authors wrote the manuscript.

Competing interests

S.S.S.-O. is a scientific adviser and holds equity in CytoReason. All other authors declare no competing interests.

Corresponding author

Correspondence to Shai S Shen-Orr.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–10 and Supplementary Notes 1–5

  2. 2.

    Life Sciences Reporting Summary

Excel files

  1. 1.

    Supplementary Table 1

    Functional enrichment of embryonic and maternal gene-clusters

  2. 2.

    Supplementary Table 2

    Antibodies used for mass cytometry experiment

Zip files

  1. 1.

    Supplementary Software

    cellAlign package