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

Data Set: UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Siamak GN Accession: GN867 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 trakhtenberg@uchc.edu Website Download datasets and supplementary data files

Specifics of this Data Set:

Siamak normalization mapped to our DB

Summary:

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. https://www.nature.com/articles/s41467-018-05134-3

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279

• 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)
• NIDA, NIMH, and NIAAA (P20-DA 21131, 2001-2012)
• NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)