Spatial reconstruction of single-cell gene expression data View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-05

AUTHORS

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

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. More... »

PAGES

495-502

References to SciGraph publications

Journal

TITLE

Nature Biotechnology

ISSUE

5

VOLUME

33

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nbt.3192

DOI

http://dx.doi.org/10.1038/nbt.3192

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1009318815

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/25867923


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curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/nbt.3192'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/nbt.3192'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nbt.3192'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nbt.3192'


 

This table displays all metadata directly associated to this object as RDF triples.

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