Eye in a Disk 2.0: Human Pan-Eye and Body Transcriptome Database

Abstract

Purpose : Comparing gene expression levels across ocular and body tissues provides insights into that gene’s function. We previously built an interactive, web-based resource (eyeIntegration (EI)) that normalized RNA-sequencing datasets from numerous published sources to allow eye researchers to query the expression levels of any gene across various eye structures and body tissues. Here, we significantly enhance the existing resource by increasing the number of samples and types of ocular tissue represented in the database, add cell type level expression information aggregated from single cell RNA-seq resources, provide guidance for researchers to directly compare expression levels in their own RNA-seq data to our database, and create a UCSC track hub to display genome-wide base pair level expression.

Methods : We queried publicly available repositories to find healthy, non-perturbed, human eye tissue RNA-seq samples deposited between the dates of Jan. 1st, 2019 and Nov. 1st, 2022. For this iteration of EI, we added a total of 287 new ocular samples, including new choroid, conjunctiva, optic nerve, macular vs. peripheral RPE and retina, and trabecular meshwork tissue types. We also add new categories for a range of RPE culture types, both primary and induced-pluripotent stem cells. Our 1272 eye and 1391 non-eye reference GTEx samples were processed with Snakerail, our Snakemake wrapper for the Monorail RNA-seq processing pipeline. Snakerail outputs a RangedSummarizedExperiment object for each study in our dataset which we combine along with single cell data from plae.nei.nih.gov to produce a SQLite database file: the Eye in a Disk (EiaD) v2.0 dataset

Results : To enable comparisons between our database and outside data, we provide R notebook guides that demonstrates how to process outside data and bring them into a shared space to enable PCA and differential comparisons.

The EI portal provides visualization of human eye-related transcriptomes published to date by database version, gene, 31 body tissues, 11 eye tissues, and 53 cell types. The new UCSC track hub enables base pair level expression visualization across the EI v2.0 database.

Conclusions : The eyeIntegration v2.0 web app serves the pan-human eye and body transcriptome dataset, EiaD v2.0. This enhanced tool and database provides the ophthalmic community with a powerful and quick means to formulate and test hypotheses on human gene and transcript expression.

This abstract was presented at the 2023 ARVO Annual Meeting, held in New Orleans, LA, April 23-27, 2023.