Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes

Nature Communications
Bruce A RheaumeEphraim F Trakhtenberg

Abstract

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.

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Datasets Mentioned

BETA
GSE115404

Methods Mentioned

BETA
transgenic
scRNA-seq
RNA-seq
Assay
Illumina sequencing
RNA-seqs

Software Mentioned

Gene Browser
Violin Plot
CellRanger
CellView pipeline
. Net Layers
MATLAB
R package Ape
SPSS
bcl2fastq
SNE

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