EORNA v.2 barley gene and transcript abundance dataset

The growth of publicly available short read sequencing data shows no sign of abating, however, the reuse of publicly available datasets is limited which means a missed opportunity in terms of the scientific value of this vast data resource. This includes the potential for reanalysis of RNA-Seq data which can be used to quantify gene expression. Efforts have been made to quantify large volumes of public RNA-Seq data from human and mouse but there is generally little reuse of this type of data in the plant science community.

We present a major new release of the EoRNA database, a gene expression database for barley based on public data (https://ics.hutton.ac.uk/eorna2/index.html). EoRNA v.2 features an order of magnitude more samples and is based on an automated workflow of sample discovery and processing which has enabled a dramatic scale-up the original database. EORNA v.2 features a total of 171 studies comprising 6,285 sample accessions. This represents the full complement of paired-end Illumina RNA-Seq from barley in the European Nucleotide Archive (ENA) (https://www.ebi.ac.uk/ena/browser/home) as of May 2024.

A dedicated new reference transcript dataset (RTD) has been created for EoRNA v.2 which is largely based on the recently published barley pan-transcriptome and represents the most comprehensive dataset of its kind to date. This has been used for quantification of the RNA-Seq data.

Here we make available the full set of quantification data from EORNA v.2, along with the RTD used for quantification, and the linear pan-genome reference sequence the RTD is based on.  The software for the EORNA2 website and database are available at https://doi.org/10.5281/zenodo.18956827.

For further details please refer to the cited publication below.  

The files we release here are as follows:

1.      EORNA2_allTPMs_geneLevel.txt.zip: The quantification data in TPM (Transcripts Per Million) as produced by Salmon, the quantification tool used (https://doi.org/10.1038/nmeth.4197). The data is a square matrix in tab delimited text format with a single header line. Genes in rows, samples in columns. Sample identifiers are run accession IDs from the European Nucleotide Archive (ENA). TPM values from individual transcripts of the same gene have been summed to produce a single value per gene x sample combination.

2.      EORNA2_allTPMs_transcriptLevel.txt.zip: as above for file 1, but rows represent transcripts rather than genes, i.e. each value represents a single transcript x sample combination.

3.      EoRNA2_metadata_run_accessions.txt: manually curated metadata of the run accessions from the ENA.

4.      EoRNA2_metadata_study_accessions.txt: manually curated metadata of the study accessions from the ENA.

5.      EoRNA2_RTD_functionalAnnotation.zip: gene-level functional annotation for genes in the EORNA v.2 reference transcript dataset. Includes GO annotation from TRAPID, Pannzer and AHRD. See publication for details.

6.      EoRNA2_RTD_gtf.zip: GTF file with gene models for EoRNA2_RTD.

7.      EoRNA2_RTD_proteins_fasta.zip: protein translations for transcripts in EoRNA2_RTD.

8.      EoRNA2_RTD_transcripts_fasta.zip: transcript sequences for EoRNA2_RTD.

9.      PSVCP_20Pangenome_fasta.gz: the linear pan-genome reference sequence used for the construction of EoRNA2_RTD.