June 2022
Volume 63, Issue 7
Open Access
ARVO Annual Meeting Abstract  |   June 2022
Spectacle: A Platform for Interacting with Over 1.5 Million Single-Cell Expression Profiles from the Eye
Author Affiliations & Notes
  • Andrew P Voigt
    University of Iowa Institute for Vision Research, Iowa City, Iowa, United States
    Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, United States
  • Nicholas D Lessing
    University of Iowa Institute for Vision Research, Iowa City, Iowa, United States
    Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, United States
  • Edwin M Stone
    University of Iowa Institute for Vision Research, Iowa City, Iowa, United States
    Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, United States
  • Budd A. Tucker
    University of Iowa Institute for Vision Research, Iowa City, Iowa, United States
    Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, United States
  • Robert F Mullins
    University of Iowa Institute for Vision Research, Iowa City, Iowa, United States
    Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, United States
  • Todd E Scheetz
    University of Iowa Institute for Vision Research, Iowa City, Iowa, United States
    Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, United States
  • Footnotes
    Commercial Relationships   Andrew Voigt None; Nicholas Lessing None; Edwin Stone None; Budd Tucker None; Robert Mullins None; Todd Scheetz None
  • Footnotes
    Support  NIH Grant EY031923
Investigative Ophthalmology & Visual Science June 2022, Vol.63, 1172 – A0026. doi:
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      Andrew P Voigt, Nicholas D Lessing, Edwin M Stone, Budd A. Tucker, Robert F Mullins, Todd E Scheetz; Spectacle: A Platform for Interacting with Over 1.5 Million Single-Cell Expression Profiles from the Eye. Invest. Ophthalmol. Vis. Sci. 2022;63(7):1172 – A0026.

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      © ARVO (1962-2015); The Authors (2016-present)

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Abstract

Purpose : Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of ocular gene expression. However, analysis of scRNA-seq data is time consuming and requires a degree of bioinformatic expertise. We developed the free online platform Spectacle to provide rapid, interactive access to scRNA-seq data. Spectacle contains over thirty fully processed datasets that collectively contain 1.5 million cells across the cornea, iris, limbus, trabecular meshwork, retina, retinal organoids, RPE, choroid, and sclera.

Methods : We reprocessed scRNA-seq data from thirty-one previously published ocular scRNA-seq manuscripts with our R package cellcuratoR, which transforms expression matrices into interactive objects within R Shiny. For over 90% of datasets, the exact clustering coordinates have been recaptured, which simplifies comparison with figures from existing manuscripts.

Results : Like other scRNA-seq visualization tools, Spectacle supports interactive exploration of cell clustering and gene expression through dot plots, heatmaps, and violin plots. However, a growing number of scRNA-seq studies compare gene expression across different biological conditions. Spectacle uniquely supports such studies and facilitates sophisticated, biologically driven analyses. For example, Spectacle powers flexible differential expression to identify genes enriched with different biological conditions (e.g., health versus disease) (Figure 1). In addition, cells can be reclustered to search for rare subpopulations of cells with certain biological characteristics. Finally, Spectacle can simultaneously compare gene expression across multiple different data sets, increasing confidence that a gene is expressed in a particular cell type or enriched with a particular biological feature (e.g., enriched in foveal retinal cells). Spectacle is freely accessible online at https://singlecell-eye.org.

Conclusions : Spectacle is a free, interactive resource that powers sophisticated, user-driven biological analyses with a very large collection of ocular scRNA-seq studies.

This abstract was presented at the 2022 ARVO Annual Meeting, held in Denver, CO, May 1-4, 2022, and virtually.

 

A screenshot of Spectacle shows differential expression between choroidal endothelial cells from nine healthy donor maculas (blue) and nine early atrophic AMD maculas (red). Differential expression results can be exported in both graphical and tabular formats.

A screenshot of Spectacle shows differential expression between choroidal endothelial cells from nine healthy donor maculas (blue) and nine early atrophic AMD maculas (red). Differential expression results can be exported in both graphical and tabular formats.

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