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Data Set Group2: UConn-Rheaume Retina RGC (Sep18) scRNA-Seq modify this page

Data Set: UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Raw modify this page
GN Accession: GN865
GEO Series: GSE115404
Title: Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes
Organism: Mouse (Mus musculus, mm10)
Group: Retina-RGC-Rheaume
Tissue: Retina Single-cell RNA-Seq
Dataset Status: Public
Platforms: SOLID-BasicGencode-Ensembl82-2015-10-02.bed
Normalization: RNA-seq
Contact Information
Bruce A. Rheaume
University of Connecticut School of Medicine
263 Farmington Ave
Farmington, CT 06030 USA
Tel. 860-679-7819
Download datasets and supplementary data files

Specifics of this Data Set:
Raw data


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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GeneNetwork support from:
  • The UT Center for Integrative and Translational Genomics
  • NIGMS Systems Genetics and Precision Medicine project (R01 GM123489, 2017-2021)
  • NIDA NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
  • NIA Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
  • NIAAA Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
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