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Nat Biotechnol. 2018 Jun;36(5):411-420. doi: 10.1038/nbt.4096. Epub 2018 Apr 2.

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

Author information

1
New York Genome Center, New York, New York, USA.
2
Center for Genomics and Systems Biology, New York University, New York, New York, USA.

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.

PMID:
29608179
DOI:
10.1038/nbt.4096

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