Brief Communication | Published:

Single-cell sequencing of the small-RNA transcriptome

Nature Biotechnology volume 34, pages 12641266 (2016) | Download Citation

Abstract

Little is known about the heterogeneity of small-RNA expression as small-RNA profiling has so far required large numbers of cells. Here we present a single-cell method for small-RNA sequencing and apply it to naive and primed human embryonic stem cells and cancer cells. Analysis of microRNAs and fragments of tRNAs and small nucleolar RNAs (snoRNAs) reveals the potential of microRNAs as markers for different cell types and states.

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Acknowledgements

We thank J. Muhr and D. Topcic (Ludwig Institute for Cancer Research, Stockholm) for providing glioblastoma cells, and W. Kang for constructive comments on the computational pipeline. This work was supported by Knut and Alice Wallenberg Foundation (2015.0096) (F.L.), the Swedish Research Council (F.L. and R.S.), Ragnar Söderberg Foundation (F.L.), the Swedish Foundation for Strategic Research (F.L. and R.S.), the Bert L. and N. Kuggie Vallee Foundation (R.S.) and the European Research Council (648842) (R.S.).

Author information

Author notes

    • Omid R Faridani
    •  & Ilgar Abdullayev

    These authors contributed equally to this work.

Affiliations

  1. Ludwig Institute for Cancer Research, Stockholm, Sweden.

    • Omid R Faridani
    • , Ilgar Abdullayev
    • , Michael Hagemann-Jensen
    •  & Rickard Sandberg
  2. Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

    • Ilgar Abdullayev
    •  & Rickard Sandberg
  3. Respiratory Medicine Unit, Department of Medicine, Solna & Center for Molecular Medicine, Stockholm, Sweden.

    • Michael Hagemann-Jensen
  4. Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden.

    • John P Schell
    •  & Fredrik Lanner
  5. Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden.

    • John P Schell
    •  & Fredrik Lanner

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Contributions

O.R.F. conceived the study, developed the method, interpreted the results and prepared the manuscript. I.A. constructed the bioinformatics pipeline, analyzed the data, prepared the figures and contributed to manuscript text. M.H.-J. helped optimize the protocol and constructed libraries, J.P.S. and F.L. contributed naive and primed embryonic stem cells. R.S. supervised the development of the method and the computational analyses, and prepared the manuscript.

Competing interests

O.R.F. and R.S. have filed a patent application on the protocol for single-cell small-RNA sequencing.

Corresponding authors

Correspondence to Omid R Faridani or Rickard Sandberg.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–12 and Supplementary Tables 1 and 2

Excel files

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    Supplementary Table 3

    Sequencing statistics of single-cell small RNA libraries

Zip files

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    Supplementary Software

    Python scripts for processing the small-RNA sequence library data

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DOI

https://doi.org/10.1038/nbt.3701

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