Journal
NATURE BIOTECHNOLOGY
Volume 33, Issue 5, Pages 503-U215Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/nbt.3209
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Funding
- European Molecular Biology Laboratory
- EMBL International PhD Programme
- EMBL Interdisciplinary Postdoc Programme under Marie Curie Actions COFUND
- Wellcome Trust Sanger Institute
- European Union's Seventh Framework Programme [ERCEA-AdG-2011-294810_'BrainEvoDevo']
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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.
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