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Integrating single-cell transcriptomic data across different conditions, technologies, and species

Nature Biotechnology volume 36, pages 411–420 (2018)Cite this article

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Abstract

Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied to experiments representing a single condition, technology, or species to discover and define cellular phenotypes. However, identifying subpopulations of cells that are present across multiple data sets remains challenging. Here, we introduce an analytical strategy for integrating scRNA-seq data sets based on common sources of variation, enabling the identification of shared populations across data sets and downstream comparative analysis. We apply this approach, implemented in our R toolkit Seurat (http://satijalab.org/seurat/), to align scRNA-seq data sets of peripheral blood mononuclear cells under resting and stimulated conditions, hematopoietic progenitors sequenced using two profiling technologies, and pancreatic cell 'atlases' generated from human and mouse islets. In each case, we learn distinct or transitional cell states jointly across data sets, while boosting statistical power through integrated analysis. Our approach facilitates general comparisons of scRNA-seq data sets, potentially deepening our understanding of how distinct cell states respond to perturbation, disease, and evolution.

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Figure 1: Overview of Seurat alignment of single-cell RNA-seq data sets.
Figure 2: Integrated analysis of resting and stimulated PBMCs.
Figure 3: Comparative analysis of mouse hematopoietic progenitors across scRNA-seq technologies.
Figure 4: Joint identification of cell types across human and mouse islet scRNA-seq atlases.
Figure 5: Benchmarking alignment and batch correction methods.

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Acknowledgements

We thank members of the Satija laboratory, as well as P. Roelli, M. Stoeckius, G. Fishell, C. Desplan, R. Bonneau, E. Macosko, and A. Corvelo for their valuable feedback, and F. Hamey, HM Kang, and J. Ye for assistance with published data sets. This work was supported by an NIH New Innovator Award (1DP2HG009623-01) and R01 (5R01MH071679-12) to R.S. and an NSF Graduate Fellowship (DGE1342536) to A.B.

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Authors and Affiliations

  1. New York Genome Center, New York, New York, USA

    Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi & Rahul Satija

  2. Center for Genomics and Systems Biology, New York University, New York, New York, USA

    Andrew Butler, Efthymia Papalexi & Rahul Satija

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  2. Paul Hoffman
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Contributions

A.B. and R.S. conceived the research. A.B., P.H., and R.S. implemented the alignment procedure, performed all data analysis, and wrote the manuscript. E.P. performed the PBMC validation experiments, and P.S. performed the ddSeq experiments.

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Correspondence to Rahul Satija.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–15 (PDF 8713 kb)

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Supplementary Dataset 1

Cell metadata for IFNB response analysis (TXT 681 kb)

Supplementary Dataset 2

Cell metadata for murine hematopoiesis analysis (TXT 83 kb)

Supplementary Dataset 3

Cell metadata for cross-species pancreatic islet analysis (TXT 545 kb)

Supplementary Dataset 4

This table contains a summary of the data distributions and statistical details related to the manuscript figures (XLSX 32 kb)

Supplementary Software

Source code and installation instructions for software used in described analyses (ZIP 810 kb)

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Butler, A., Hoffman, P., Smibert, P. et al. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol 36, 411–420 (2018). https://doi.org/10.1038/nbt.4096

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