Spectacle Citation: if you use Spectacle or cellcuratoR for your research, please consider citing the manuscript that describes this platform:

Spectacle: An interactive resource for ocular single-cell RNA sequencing data analysis. Experimental Eye Research, September 2020. PMID: 32910939

Dataset Citation: if you use expression data from a Spectacle dataset, please consider citing that dataset (citation information below).

Molecular characterization of foveal versus peripheral human retina by single-cell RNA sequencing. Experimental Eye Research, May 2019. PMID: 31075224

Dataset name: retina_fov_vs_periph

Tissue: retina
Donors: 3 (paired)
Libraries: paired foveal and peripheral
Recovered Cells: 8217

Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration. Proceedings of the National Academy of Sciences, November 2019. PMID: 31712411

Dataset name: RPE_chor_unselected

Tissue: RPE and choroid, no pre-enrichment
Donors: 3 (paired)
Libraries: paired macular and peripheral
Recovered Cells: 4355

Dataset name: RPE_chor_CD31_selected

Tissue: RPE and choroid, CD31-enrichment of endothelial cells
Donors: 4 (paired)
Libraries: paired macular and peripheral
Recovered Cells: 14,234

Single-Cell RNA Sequencing in Human Retinal Degeneration Reveals Distinct Glial Cell Populations. Cells, February 2020. PMID: 32069977

Dataset name: retina_AIR_vs_control

Tissue: retina
Donors: 5 (paired), including one donor with autoimmune retinopathy (AIR)
Libraries: paired foveal and peripheral, one paired library from AIR patient
Recovered Cells: 23,429

Bulk and Single-Cell Gene Expression Analyses Reveal Aging Human Choriocapillaris Has Pro-Inflammatory Phenotype. Microvascular Research, June 2020. PMID: 32531351

Dataset name: CD31_choroid_infant_adult

Tissue: RPE and choroid, CD31-enrichment of endothelial cells
Donors: 8 (2 infant, 6 adults)
Libraries: 4 paired macular/peripheral, 4 paired CD31-positive/CD31-negative
Recovered Cells: 37,070

Human photoreceptor cells from different macular subregions have distinct transcriptional profiles. Human Molecular Genetics, May 2021. PMID: 34014299

Dataset name: retina_fovea_perifovea

Tissue: Foveal (1 mm) and parafoveal (4 mm) retina
Donors: 4
Libraries: 4 paired foveal/parafoveal
Recovered Cells: 34,493

All Seurat-analyzed datasets (in .RData files) are publically available at https://oculargeneexpression.org/pages/methods_tech.html

Spectacle and its enclosed datasets are made possible with generous funding from:

The National Institute of Health: EY027038, EY024605, EY025580, EY031923, GM007337

The Roy J. Carver, Jr. Chair in Bioinformatics and Computational Biology (Todd Scheetz)

The Martin Carver Chair in Ocular Cell Biology (Rob Mullins)

The Elmer and Sylvia Sramek Charitable Foundation

Research to Prevent Blindness

Institute for Vision Research Advisory Board

Spectacle v0.1.0 (bifocals)

v0.1.0: September 7, 2020

  • First release corresponding to the manuscript described in Experimental Eye Research.
  • v0.2.0: December 9, 2020

  • Introduced a toggle for gene expression to be explored in 'cartoon' form. Under the heat map tab, the user may request to visualize the average gene expression for each cell population overlaid with a cartoon drawing of the retina and/or RPE/choroid. This is more intuitive for the user and decreases plot rendering time (as tens of thousands of points do not need to re-render for each new gene being queried).
  • Added all_retina_rpe_chor dataset; which used canonical correlation analysis to integrate cells from all currently published studies.
  • Added 'quick start' documentation that is visible upon loading Spectacle.
  • v0.2.1: December 17, 2020

  • Fixed violin plot for the all_retina_rpe_chor dataset that misordered cell types on the dendrogram.
  • v0.3.0: February 6, 2021

  • NEW DATASET: added foveal (1 mm) vs parafoveal (4 mm) human retina (8 paired samples from 4 donors).
  • NEW FEATURE: added regional expression explorer, which can be accessed from the lefthand menu, to compare regional gene expression across 6 datasets.
  • Moved Spectacle to a new server, eliminating very slow loading times or connection timeouts from some internet providers.
  • Removed 'server timeouts' feature, making all plots fully interactive.
  • Added link to Mullins laboratory webpage.
  • v0.3.1: March 17, 2021

  • Fixed violin plot bug that prevented genes names with hyphens from rendering.

  • Spectacle v1.0.0 (aviators)

    v1.0.0: July 4, 2021

  • Re-coded Spectacle features into Shiny modules, condensing code and improving efficiency.
  • NEW FEATURE: added dual-expression feature, which allows the user to visualize coexpression of two genes. To access, the user must (1) load a dataset, (2) select the heatmap tab, (3) de-select the cartoon visualization slider, (4) activate the coexpression slider.
  • Modified differential expression to include a maximum of 500 cells per identity (FindMarkers(max.cells.per.ident = 500)). This accelerates differential expression with minimal changes to results.
  • Biological variables such as region and disease status can be used to color cells. Options are displayed in the `color cells` dropdown menu beneath the Dimensionality Reduction Plot (or Reclustering Plot).
  • If a gene has zero expression across all cells, all dots in the heatmap are colored grey.
  • Improved handling of point sizes and legend labels.
  • University of Iowa: Institute for Vision Research

    Spectacle and cellcuratoR were developed by an interdisciplinary team within the Institute for Vision Research at the University of Iowa. The Institute of Vision Research is deeply dedicated to treating and curing visual diseases. More information can be found at our website ivr.uiowa.edu

    If you have questions or comments for the Spectacle team, please email us at: spectacle.iowa@gmail.com

    Powered by cellcuratoR

    cellcuratoR is an R package for sharing interactive single-cell expression data from Seurat. Any single-cell RNA sequencing dataset processed with Seurat (v3) can be converted into objects interpretable by cellcuratoR. Code and documentation are available at github/drewvoigt10/cellcuratoR as well as animated instructions for navigating the user interface.