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dc.contributor.authorSatija, Rahulen_US
dc.contributor.authorFarrell, Jeffrey A.en_US
dc.contributor.authorGennert, Daviden_US
dc.contributor.authorSchier, Alexander F.en_US
dc.contributor.authorRegev, Aviven_US
dc.date.accessioned2015-12-04T18:15:27Z
dc.date.issued2015en_US
dc.identifier.citationSatija, 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.en
dc.identifier.issn1087-0156en
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:23845348
dc.description.abstractSpatial 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.en
dc.language.isoen_USen
dc.relation.isversionofdoi:10.1038/nbt.3192en
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4430369/pdf/en
dash.licenseLAAen_US
dc.titleSpatial reconstruction of single-cell gene expressionen
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden
dc.relation.journalNature biotechnologyen
dash.depositing.authorFarrell, Jeffrey A.en_US
dc.date.available2015-12-04T18:15:27Z
dc.identifier.doi10.1038/nbt.3192*
dash.contributor.affiliatedFarrell, Jeffrey
dash.contributor.affiliatedSchier, Alexander


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