Our goal is to provide access to our well-curated set of expression data from human ocular tissues for both educational and research use. Over the past decades, we have been performing experiments to elucidate the biology of vision, and the underlying etiology that results in a variety of inherited eye diseases. In that time we have transitioned our methods as the technology matured, from cDNA sequencing, through microarrays, and now with RNA sequencing from bulk tissue samples (RNA-seq) and RNA sequencing from individual cells isolated from a tissue sample (scRNA-seq).
While many expression studies have been performed on ocular tissues, in this resource we are only presenting those that we have performed at the University of Iowas Institute for Vision Research. This allows us to have consistent methods spanning sample procurement, tissue isolation, cell suspension, library preparation, and data analysis.
Components of OcularGeneExpression.org
OcularGeneExpression is a collection of 5 types of information:
Single-cell RNA-seq
The heart of the site, along with the Bulk RNA-seq section, the single-cell RNA-seq section provides access to Spectacle, a web-based interface to our ocular single-cell RNA-seq datasets. This leverages the CellCuratoR package (https://www.github.com/drewvoigt10/cellcuratoR) to summarize the data from a Seurat-analyzed dataset, and provides interfaces for users to: evaluate gene expression at the level of individual cells and clusters (typically cell types - e.g. cone photoreceptors); perform differential expression among clusters and samples; perform dimensionality reduction (e.g. tSNE) on a subset of cells to identify sub-populations within a given cell type (e.g. ON cone bipolar cells); and visualization of gene expression in form of heatmaps and violin plots.
Bulk RNA-seq (coming soon)
This section will include the data from our other ocular expression RNA-seq experiments.
Methods and Technology (coming soon)
This section describes the underlying technologies used in RNA-seq and scRNA-seq, as well as describing the methods we use for data analysis.
Data Availability (coming soon)
This section provides links to the various datasets presented in the OcularGeneExpression resource. These include links to NCBIs Gene Expression Omnibus (GEO) as well as the raw data (when available) in NCBIs Short-Read Archive (SRA).
OcularGeneExpression Team
Dr. Robert Mullins
Dr. Todd Scheetz
Dr. S. Scott Whitmore
Drew Voigt
Nick Lessing