Abstract
PURPOSE To develop an easily accessible and reliable RNA-seq transcriptome database of healthy human eye tissues and a matching reactive web application to query gene expression in eye and body tissues.
METHODS We downloaded the raw sequnce data for 892 RNA-seq samples across 44 tissues in the GTEx project as a non-eye reference set. We then queried several public repositories to find all healthy, non-perturbed, human eye-related tissue RNA-seq samples. The 1311 total samples we found were sent into a Snakemake-based reproducible pipeline we wrote to quantify all known transcripts and genes, removes samples with poor sequence quality and mislabels, normalizes expression values across each tissue, performs 450 differential expression tests, calculates GO term enrichment, and outputs all as a single SQLite database file: the Eye in a Disk (EiaD) dataset. Furthermore, we rewrote the web application eyeIntegration (https://eyeIntegration.nei.nih.gov) to display EiaD.
RESULTS The new eyeIntegration portal provides quick visualization of human eye-related transcriptomes published to date, by database version, gene/transcript, and 58 tissues. As a test of the value of this unified pan-eye dataset, we showed that fetal and organoid retina are highly similar at a pan-transcriptome level but display distinct differences in certain pathways and gene families like protocadherin and HOXB family members.
CONCLUSION The eyeIntegration v1.0 web app serves the pan-human eye and body transcriptome dataset, EiaD. This offers the eye community a powerful and quick mean to testing hypotheses on human gene and transcript expression across 44 body and 14 eye tissues.
