Integrated genome and transcriptome sequencing of the same cell

Abstract

Single-cell genomics and single-cell transcriptomics have emerged as powerful tools to study the biology of single cells at a genome-wide scale. However, a major challenge is to sequence both genomic DNA and mRNA from the same cell, which would allow direct comparison of genomic variation and transcriptome heterogeneity. We describe a quasilinear amplification strategy to quantify genomic DNA and mRNA from the same cell without physically separating the nucleic acids before amplification. We show that the efficiency of our integrated approach is similar to existing methods for single-cell sequencing of either genomic DNA or mRNA. Further, we find that genes with high cell-to-cell variability in transcript numbers generally have lower genomic copy numbers, and vice versa, suggesting that copy number variations may drive variability in gene expression among individual cells. Applications of our integrated sequencing approach could range from gaining insights into cancer evolution and heterogeneity to understanding the transcriptional consequences of copy number variations in healthy and diseased tissues.

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Figure 1: Schematic of DR-Seq.
Figure 2: Development of a computational technique to reduce technical noise in DR-Seq data and comparison of DR-Seq to existing single-cell gDNA or mRNA sequencing methods in E14 cells.
Figure 3: DR-Seq on SK-BR-3 cells.

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Acknowledgements

We would like to thank C. Zong (Harvard University) for sharing details of MALBAC and D. Grün (Hubrecht Institute) for assistance in data analysis. We would also like to thank N. Crosetto (Hubrecht Institute) for assistance in preparing DNA FISH probes. This work was supported by the European Research Council Advanced grant (ERC-AdG 294325-GeneNoiseControl), the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) Vici award and by the Human Frontier Science Program (to M.B.).

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S.S.D., L.K. and A.v.O. conceived the method. S.S.D. and L.K. performed experiments. M.B. performed DNA FISH. S.S.D. and B.S. analyzed the data. S.S.D., L.K., B.S. and A.v.O. wrote the manuscript. A.v.O. guided experiments and data analysis.

Corresponding author

Correspondence to Alexander van Oudenaarden.

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The authors declare no competing financial interests.

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Supplementary Text and Figures

Supplementary Figures 1–29, Supplementary Tables 1–5 and Supplementary Note (PDF 1620 kb)

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Dey, S., Kester, L., Spanjaard, B. et al. Integrated genome and transcriptome sequencing of the same cell. Nat Biotechnol 33, 285–289 (2015). https://doi.org/10.1038/nbt.3129

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