Gene

Cell type

Cell biology

Molecular biology

Neuroscience

Biology

Retina

Retinal

Biochemistry

Environmental health

Immunostaining

Immunology

Genetics

Transcriptome

In situ hybridization

Population

Retinal ganglion cell

Medicine

Cell

Gene expression profiling

Immunohistochemistry

Gene expression

Nature Communications

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.

Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes