BrassicaEDB

BrassicaEDB integrates RNA sequencing (RNA-Seq) expression data for Brassica napus to enable transcriptome-level analysis of approximately 101,040 genes across 103 tissues from seven developmental stages of the cultivar ZhongShuang11 (ZS11) and across 70 SRA BioProjects, providing Fragments Per Kilobase Million (FPKM), Transcripts Per Million (TPM), raw read counts and eFP visualization.

Key Features:

• Comprehensive ZS11 RNA-Seq dataset: Expression data derived from 103 tissues across seven developmental stages (seed germination, seedling, bolting, initial flowering, full-bloom, podding, maturation) of Brassica napus cultivar ZhongShuang11 (ZS11) covering ~101,040 genes.
• Multiple expression metrics: Provision of Fragments Per Kilobase Million (FPKM), Transcripts Per Million (TPM), and raw read counts for quantitative analyses.
• eFP Module: Visualization of gene expression profiles across tissues and developmental stages using the eFP browser.
• Treatment Module: Examination of gene expression responses to experimental treatments for functional genomics studies.
• Coexpression Module: Identification of coexpressed genes to support network analysis and pathway elucidation.
• SRA Project Module: Integration of transcriptome data from 70 BioProjects in the Sequence Read Archive (SRA) with access to raw and processed data.
• Gene Feature Module: Compilation of genomic features, annotations, and functional predictions linked to genes of interest.
• qPCR Primer Module: Provision of validated primers for quantitative PCR experimental validation.
• BLAST Module: Sequence similarity searches against a curated database for gene identification and comparative genomics.

Scientific Applications:

• Developmental expression profiling: Analysis of gene expression dynamics across seven developmental stages of Brassica napus.
• Treatment response analysis: Investigation of transcriptomic responses to experimental treatments for functional inference.
• Coexpression and network analysis: Discovery of coexpressed gene modules for pathway and regulatory network studies.
• Comparative transcriptomics: Cross-study comparisons using integrated data from 70 SRA BioProjects.
• Experimental validation support: Selection of qPCR primers for validating transcriptomic findings.
• Gene identification and annotation: Use of BLAST searches for sequence-based gene identification and comparative analysis.

Methodology:

Integration of RNA-Seq data from 103 tissues across seven developmental stages of ZS11 and from 70 SRA BioProjects, calculation/provision of FPKM, TPM and raw read counts, and visualization of expression results via the eFP browser.