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Quantitative single-cell RNA-seq with unique molecular identifiers

Nature Methods volume 11, pages 163–166 (2014)Cite this article

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Abstract

Single-cell RNA sequencing (RNA-seq) is a powerful tool to reveal cellular heterogeneity, discover new cell types and characterize tumor microevolution. However, losses in cDNA synthesis and bias in cDNA amplification lead to severe quantitative errors. We show that molecular labels—random sequences that label individual molecules—can nearly eliminate amplification noise, and that microfluidic sample preparation and optimized reagents produce a fivefold improvement in mRNA capture efficiency.

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Figure 1: Molecule counting using UMIs.
Figure 2: Reproducibility of molecule counting.
Figure 3: Transcriptional noise in ES cells.

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Gene Expression Omnibus

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Acknowledgements

Illumina sequencing experiments were performed by A. Johnsson and A. Juréus (Karolinska Institutet). ES cells were generously provided by the Karolinska Center for Transgene Technologies. Recombinant Tn5 transposase was a generous gift from R. Sandberg (Karolinska Institutet). We are grateful for the advice and support of B. Jones and B. Fowler (Fluidigm). This work was supported by grants from the Swedish Research Council (STARGET) and the European Research Council (261063) to S.L. and from the Swedish Cancer Society, Swedish Research Council and Ragnar Söderberg Foundation to M.K.

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Authors and Affiliations

  1. Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden

    Saiful Islam, Amit Zeisel, Gioele La Manno, Pawel Zajac, Peter Lönnerberg & Sten Linnarsson

  2. Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden

    Simon Joost & Maria Kasper

Authors
  1. Saiful Islam
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  2. Amit Zeisel
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  7. Peter Lönnerberg
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Contributions

S.L. conceived the study. S.I., A.Z. and P.Z. developed the protocols and performed the RNA-seq experiments. S.J. and M.K. prepared cells. A.Z., G.L.M. and S.I. developed the tagmentation protocol. P.L. wrote the bioinformatics pipeline. P.L., S.L. and A.Z. analyzed data. S.L. and S.I. wrote the manuscript with support from all authors.

Corresponding author

Correspondence to Sten Linnarsson.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–13 and Supplementary Note (PDF 1466 kb)

Supplementary Table 1

List of noisy genes (XLSX 42 kb)

Supplementary Table 2

List of custom oligonucleotides (XLSX 14 kb)

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Islam, S., Zeisel, A., Joost, S. et al. Quantitative single-cell RNA-seq with unique molecular identifiers. Nat Methods 11, 163–166 (2014). https://doi.org/10.1038/nmeth.2772

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