title: High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin.
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.
authors: 1] European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK. [2] Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
authors: Kaia
authors: 0000000337234065
authors: K
authors: Achim
authors: European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK.
authors: Jean-Baptiste
authors: JB
authors: Pettit
authors: 1] European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK. [2] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK.
authors: Luis R
authors: 0000000340790396
authors: LR
authors: Saraiva
authors: Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
authors: Daria
authors: D
authors: Gavriouchkina
authors: Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
authors: Tomas
authors: T
authors: Larsson
authors: Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
authors: Detlev
authors: D
authors: Arendt
authors: 1] European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK. [2] Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. [3] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK.
authors: John C
authors: JC
authors: Marioni
mesh_terms: D000818:Animals; D018507:Gene Expression Regulation, Developmental; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D009928:Organ Specificity / Q000235:genetics; D011077:Polychaeta / Q000235:genetics* / Q000254:growth & development; D059010:Single-Cell Analysis / Q000379:methods*; D059467:Transcriptome / Q000235:genetics