Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes

Nat Commun. 2018 Jul 17;9(1):2759. doi: 10.1038/s41467-018-05134-3.


Retinal ganglion cells (RGCs) convey the major output of information collected from the eye to the brain. Thirty subtypes of RGCs have been identified to date. Here, we analyze 6225 RGCs (average of 5000 genes per cell) from right and left eyes by single-cell RNA-seq and classify them into 40 subtypes using clustering algorithms. We identify additional subtypes and markers, as well as transcription factors predicted to cooperate in specifying RGC subtypes. Zic1, a marker of the right eye-enriched subtype, is validated by immunostaining in situ. Runx1 and Fst, the markers of other subtypes, are validated in purified RGCs by fluorescent in situ hybridization (FISH) and immunostaining. We show the extent of gene expression variability needed for subtype segregation, and we show a hierarchy in diversification from a cell-type population to subtypes. Finally, we present a website for comparing the gene expression of RGC subtypes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Animals, Newborn
  • Cell Lineage / genetics*
  • Core Binding Factor Alpha 2 Subunit / genetics
  • Core Binding Factor Alpha 2 Subunit / metabolism
  • Eye Proteins / genetics*
  • Eye Proteins / metabolism
  • Follistatin / genetics
  • Follistatin / metabolism
  • Gene Expression
  • Gene Expression Profiling
  • In Situ Hybridization, Fluorescence
  • Mice
  • Mice, Inbred C57BL
  • Retinal Ganglion Cells / classification*
  • Retinal Ganglion Cells / cytology
  • Retinal Ganglion Cells / metabolism*
  • Single-Cell Analysis
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transcriptome*


  • Core Binding Factor Alpha 2 Subunit
  • Eye Proteins
  • Follistatin
  • Runx1 protein, mouse
  • Transcription Factors
  • Zic1 protein, mouse