High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin View Full Text


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Article Info

DATE

2015-05

AUTHORS

Kaia Achim, Jean-Baptiste Pettit, Luis R Saraiva, Daria Gavriouchkina, Tomas Larsson, Detlev Arendt, John C Marioni

ABSTRACT

Understanding cell type identity in a multicellular organism requires the integration of gene expression profiles from individual cells with their spatial location in a particular tissue. Current technologies allow whole-transcriptome sequencing of spatially identified cells but lack the throughput needed to characterize complex tissues. Here we present a high-throughput method to identify the spatial origin of cells assayed by single-cell RNA-sequencing within a tissue of interest. Our approach is based on comparing complete, specificity-weighted mRNA profiles of a cell with positional gene expression profiles derived from a gene expression atlas. We show that this method allocates cells to precise locations in the brain of the marine annelid Platynereis dumerilii with a success rate of 81%. Our method is applicable to any system that has a reference gene expression database of sufficiently high resolution. More... »

PAGES

503-509

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nbt.3209

DOI

http://dx.doi.org/10.1038/nbt.3209

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1004892473

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/25867922


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curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/nbt.3209'

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.3209'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nbt.3209'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nbt.3209'


 

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

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