Spatial reconstruction of single-cell gene expression data

Rahul Satija, Jeffrey A. Farrell, David Gennert, Alexander F. Schier, Aviv Regev

Research output: Contribution to journalArticle

Abstract

Spatial localization is a key determinant of cellular fate and behavior, but methods for spatially resolved, transcriptome-wide gene expression profiling across complex tissues are lacking. RNA staining methods assay only a small number of transcripts, whereas single-cell RNA-seq, which measures global gene expression, separates cells from their native spatial context. Here we present Seurat, a computational strategy to infer cellular localization by integrating single-cell RNA-seq data with in situ RNA patterns. We applied Seurat to spatially map 851 single cells from dissociated zebrafish (Danio rerio) embryos and generated a transcriptome-wide map of spatial patterning. We confirmed Seurat's accuracy using several experimental approaches, then used the strategy to identify a set of archetypal expression patterns and spatial markers. Seurat correctly localizes rare subpopulations, accurately mapping both spatially restricted and scattered groups. Seurat will be applicable to mapping cellular localization within complex patterned tissues in diverse systems.

Original languageEnglish (US)
Pages (from-to)495-502
Number of pages8
JournalNature Biotechnology
Volume33
Issue number5
DOIs
StatePublished - May 12 2015

Fingerprint

RNA
Gene expression
Gene Expression
Zebrafish
Transcriptome
Tissue
Gene Expression Profiling
Assays
Embryonic Structures
Staining and Labeling

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Biotechnology
  • Molecular Medicine
  • Bioengineering
  • Biomedical Engineering

Cite this

Satija, R., Farrell, J. A., Gennert, D., Schier, A. F., & Regev, A. (2015). Spatial reconstruction of single-cell gene expression data. Nature Biotechnology, 33(5), 495-502. https://doi.org/10.1038/nbt.3192

Spatial reconstruction of single-cell gene expression data. / Satija, Rahul; Farrell, Jeffrey A.; Gennert, David; Schier, Alexander F.; Regev, Aviv.

In: Nature Biotechnology, Vol. 33, No. 5, 12.05.2015, p. 495-502.

Research output: Contribution to journalArticle

Satija, R, Farrell, JA, Gennert, D, Schier, AF & Regev, A 2015, 'Spatial reconstruction of single-cell gene expression data', Nature Biotechnology, vol. 33, no. 5, pp. 495-502. https://doi.org/10.1038/nbt.3192
Satija, Rahul ; Farrell, Jeffrey A. ; Gennert, David ; Schier, Alexander F. ; Regev, Aviv. / Spatial reconstruction of single-cell gene expression data. In: Nature Biotechnology. 2015 ; Vol. 33, No. 5. pp. 495-502.
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