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Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling
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The Soybean Expression Atlas v2: A comprehensive database of over 5000 RNA-seq samples
Fabricio Almeida-Silva1,2, Francisnei Pedrosa-Silva3, Thiago M Venancio3
1Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
The Plant Journal : for Cell and Molecular Biology
|September 8, 2023
Summary
The Soybean Expression Atlas v2 offers enhanced gene expression data for over 5,000 RNA-seq samples, improving soybean research with new features and an accessible interface.
Area of Science:
- Plant Biology
- Genomics
- Bioinformatics
Background:
- Soybean is a vital global crop for food, feed, and industry.
- Publicly available RNA-sequencing (RNA-seq) data for soybean is rapidly accumulating.
- Computational challenges exist in processing large-scale RNA-seq datasets.
Purpose of the Study:
- To present an updated version of the Soybean Expression Atlas (v2).
- To provide researchers with enhanced gene expression data and analysis tools for soybean.
- To improve accessibility and usability of soybean transcriptomic data.
Main Methods:
- Compiled and processed 5,481 publicly available soybean RNA-seq samples.
- Generated transcript- and gene-level abundance matrices.
- Developed a reproducible and scalable analysis pipeline as an R package.
Main Results:
- Soybean Expression Atlas v2 features a fourfold increase in samples compared to the previous version.
- Includes transcript-level abundance estimates for differential transcript usage analysis.
- Offers bias-corrected counts for more accurate differential gene expression analyses.
- Features a new web interface with improved data visualization and user experience.
Conclusions:
- Soybean Expression Atlas v2 significantly expands access to high-quality soybean gene expression data.
- New features facilitate deeper insights into soybean transcriptomics and gene function.
- The database and associated tools will accelerate advancements in soybean research.
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