Soybean Expression Atlas v2

Soybean Expression Atlas v2 provides a curated collection of over 5,481 publicly available RNA-seq samples with processed transcript- and gene-level abundance matrices and bias-corrected counts to support exploration of soybean gene expression, differential transcript usage, agronomic trait–associated genes, and transcriptional dynamics.

Key Features:

• Comprehensive RNA-seq sample collection: Includes over 5,481 publicly available RNA-seq samples representing a fourfold increase in dataset size relative to the prior release.
• Transcript- and Gene-Level Transcript Abundance Matrices: Provides processed matrices for both transcript- and gene-level expression to enable multi-resolution expression analyses.
• Transcript-Level Abundance Estimates: Supplies transcript-level abundance estimates to facilitate analysis of differential transcript usage.
• Bias-Corrected Counts: Includes bias-corrected abundance counts intended to improve accuracy in differential gene expression analyses.
• Reproducible and Scalable Pipeline (R package): Distributes a reproducible and scalable analysis pipeline as an R package for processing and summarizing RNA-seq data.

Scientific Applications:

• Gene discovery for agronomic traits: Identification of genes linked to agronomic traits through expression profiling.
• Transcriptional response analysis: Characterization of transcriptional responses under different conditions using RNA-seq expression data.
• Gene family functional exploration: Exploration of functional roles of specific gene families in soybean biology via expression patterns.
• Transcriptional dynamics studies: Investigation of transcriptional dynamics involved in cellular processes using transcript- and gene-level data.

Methodology:

Provides processed transcript- and gene-level abundance matrices, transcript-level abundance estimates, and bias-corrected counts generated and packaged via a reproducible, scalable pipeline distributed as an R package.