Dataset Information

Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0.

ABSTRACT: Purpose:We develop an accessible and reliable RNA sequencing (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 sequence data for 1375 RNA-seq samples across 54 tissues in the Genotype-Tissue Expression (GTEx) project as a noneye reference set. We then queried several public repositories to find all healthy, nonperturbed, human eye-related tissue RNA-seq samples. The 916 eye and 1375 GTEx samples 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, perform 882 differential expression tests, calculate GO term enrichment, and output all as a single SQLite database file: the Eye in a Disk (EiaD) dataset. Furthermore, we rewrote the web application eyeIntegration (available in the public domain at 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, 19 eye tissues, and 54 body 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, such as protocadherin and HOXB family members. Conclusions: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 means to test hypotheses on human gene and transcript expression across 54 body and 19 eye tissues.

SUBMITTER: Swamy V

PROVIDER: S-EPMC6660187 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0.

Swamy Vinay V McGaughey David D

Investigative ophthalmology & visual science 20190701 8

<h4>Purpose</h4>We develop an accessible and reliable RNA sequencing (RNA-seq) transcriptome database of healthy human eye tissues and a matching reactive web application to query gene expression in eye and body tissues.<h4>Methods</h4>We downloaded the raw sequence data for 1375 RNA-seq samples across 54 tissues in the Genotype-Tissue Expression (GTEx) project as a noneye reference set. We then queried several public repositories to find all healthy, nonperturbed, human eye-related tissue RNA-s ...[more]

PMID: 31343654

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Project description:BackgroundConsidering the growing demand for plant trait data and taking into account the lack of trait data from Eastern Europe, especially from its steppic region, we launched a new Ukrainian Plant Trait Database (UkrTrait v. 1.0) aiming at collecting all the available plant trait data from Ukraine.To facilitate further use of this database, we linked the trait terminology to the TRY Plant Trait Database, Thesaurus of Plant Characteristics (TOP) and Plant Trait Ontology (TO). For taxa names, we provide the crosswalks between the Ukrainian checklist and international sources, i.e. GBIF Backbone Taxonomy, World Checklist of Vascular Plants (World Checklist of Vascular Plants (World Checklist of Vascular Plants (WCVP), World Flora Online (WFO) and Euro+Med PlantBase. We aim to integrate our data into the relevant global (TRY Plant Trait Database) and pan-European (FloraVeg.EU) databases. The current version of the database is freely available at the Zenodo repository and will be updated in the future.New informationUntil now, plant traits for the Ukrainian flora were scattered across literature, often focusing on single species and written mainly in Ukrainian. Additionally, many traits were in grey literature or remained non-digitised, which rendered them inaccessible to the global scientific community. Addressing this gap, our Ukrainian Plant Trait Database (UkrTrait v. 1.0) represents a significant step forward. We compiled and digitised plant traits from local Ukrainian literature sources. Furthermore, we performed our own field and laboratory measurements of various plant traits that were not previously available in literature. In the current version of the UkrTrait, we focus on vascular plant species that are absent from the other European trait databases, with emphasis on species that are representative for the steppe vegetation. Traits assembled from literature include life span (annuals, biennials, perennials), plant height, flowering period (flowering months), life form (by Raunkiaer), plant growth form and others. Our own measured traits include seed mass, seed shape, leaf area, leaf nitrogen concentration and leaf phosphorus concentration. The current version, i.e. UkrTrait v. 1.0, comprises digitised literature data of 287,948 records of 75 traits for 6,198 taxa and our own trait measurements of 2,390 records of 12 traits for 388 taxa.

Dataset Information

Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0.

Publications

Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0.

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