High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

Kaia Achim, Jean Baptiste Pettit, Luis Miguel Rodrigues Saraiva, Daria Gavriouchkina, Tomas Larsson, Detlev Arendt, John C. Marioni

Research output: Contribution to journalArticle

158 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)503-509
Number of pages7
JournalNature Biotechnology
Issue number5
Publication statusPublished - 12 May 2015
Externally publishedYes


ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Medicine(all)
  • Molecular Medicine
  • Biomedical Engineering
  • Applied Microbiology and Biotechnology

Cite this

Achim, K., Pettit, J. B., Rodrigues Saraiva, L. M., Gavriouchkina, D., Larsson, T., Arendt, D., & Marioni, J. C. (2015). High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin. Nature Biotechnology, 33(5), 503-509. https://doi.org/10.1038/nbt.3209