EoRNA

EoRNA provides quantitative gene and transcript abundance data for barley using the BaRTv1.0 (Barley Reference Transcript) dataset to support expression profiling and alternative splicing analyses.

Key Features:

• Data Presentation: Visualization of comparative gene and transcript abundance expressed in transcripts per million (TPM) across barley samples.
• Gene and Transcript Models: Comprehensive gene and transcript models from the BaRTv1.0 dataset with identifiers in BaRT and HORVU namespaces and sequence lookup via BLAST.
• Expression Insights: Expression data across barley cultivars, tissues, and conditions, including quantification of changes in transcript proportions resulting from alternative splicing.
• Data Extraction for Analysis: Extraction of TPM values for statistical evaluation of transcript abundance variation and meta-analysis across multiple RNA-seq experiments.

Scientific Applications:

• Expression profiling: Analysis of gene and transcript expression across 843 RNA-seq samples from 22 experiments to investigate gene function and regulation.
• Differential expression: Identification of differentially expressed genes and transcripts across tissues, cultivars, and conditions.
• Alternative splicing studies: Quantification of transcript proportion changes to study splicing variation and its regulatory effects.
• Comparative meta-analysis: Integration of TPM values across experiments to perform meta-analyses of expression patterns.
• Trait-related research: Support for studies linking expression and splicing variation to barley traits such as yield, stress resistance, and disease susceptibility.

Methodology:

Gene and transcript levels were quantified using the BaRTv1.0 reference transcript dataset across 22 RNA-seq experiments comprising 843 samples, with expression reported in transcripts per million (TPM); BLAST-based sequence searches and TPM extraction are provided for downstream statistical analyses.