Spatial reconstruction of single-cell gene expression

DSpace/Manakin Repository

Spatial reconstruction of single-cell gene expression

Citable link to this page

 

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

Note: Order does not necessarily reflect citation order of authors.

Citation: Satija, Rahul, Jeffrey A. Farrell, David Gennert, Alexander F. Schier, and Aviv Regev. 2015. “Spatial reconstruction of single-cell gene expression.” Nature biotechnology 33 (5): 495-502. doi:10.1038/nbt.3192. http://dx.doi.org/10.1038/nbt.3192.
Full Text & Related Files:
Abstract: Spatial localization is a key determinant of cellular fate and behavior, but spatial RNA assays traditionally rely on staining for a limited number of RNA species. In contrast, single-cell RNA-seq allows for deep profiling of cellular gene expression, but established methods separate 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, inferring a transcriptome-wide map of spatial patterning. We confirmed Seurat’s accuracy using several experimental approaches, and used it to identify a set of archetypal expression patterns and spatial markers. Additionally, 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.
Published Version: doi:10.1038/nbt.3192
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4430369/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:23845348
Downloads of this work:

Show full Dublin Core record

This item appears in the following Collection(s)

 
 

Search DASH


Advanced Search
 
 

Submitters