High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin - PubMed (original) (raw)
doi: 10.1038/nbt.3209. Epub 2015 Apr 13.
Affiliations
- PMID: 25867922
- DOI: 10.1038/nbt.3209
High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin
Kaia Achim et al. Nat Biotechnol. 2015 May.
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.
Comment in
- RNA: Putting transcriptomics in its place.
Burgess DJ. Burgess DJ. Nat Rev Genet. 2015 Jun;16(6):319. doi: 10.1038/nrg3951. Epub 2015 May 7. Nat Rev Genet. 2015. PMID: 25948245 No abstract available.
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