EORNA, a barley gene and transcript abundance database

Linda Milne, Micha Bayer, Paulo Rapazote-Flores, Claus-Dieter Mayer, Robbie Waugh, Craig G. Simpson (Lead / Corresponding author)

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Abstract

A high-quality, barley gene reference transcript dataset (BaRTv1.0), was used to quantify gene and transcript abundances from 22 RNA-seq experiments, covering 843 separate samples. Using the abundance data we developed a Barley Expression Database (EORNA*) to underpin a visualisation tool that displays comparative gene and transcript abundance data on demand as transcripts per million (TPM) across all samples and all the genes. EORNA provides gene and transcript models for all of the transcripts contained in BaRTV1.0, and these can be conveniently identified through either BaRT or HORVU gene names, or by direct BLAST of query sequences. Browsing the quantification data reveals cultivar, tissue and condition specific gene expression and shows changes in the proportions of individual transcripts that have arisen via alternative splicing. TPM values can be easily extracted to allow users to determine the statistical significance of observed transcript abundance variation among samples or perform meta analyses on multiple RNA-seq experiments. * Eòrna is the Scottish Gaelic word for Barley.

Original languageEnglish
Article number90
Number of pages10
JournalScientific Data
Volume8
Issue number1
DOIs
Publication statusPublished - 25 Mar 2021

Keywords

  • Genetic databases
  • Transcriptomics

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