Complete Arabidopsis transcriptome database

Complete Arabidopsis transcriptome database provides standardized access to microarray-based transcriptome data for Arabidopsis thaliana generated with the CATMA platform for comparative and functional analyses.

Key Features:

• Extensive Data Collection: Contains data from 53 projects comprising 1,724 hybridized samples covering 13 organs, 49 developmental conditions, 45 mutant variants, and 63 environmental scenarios.
• Standardization: All data are processed using a uniform protocol from microarray printing through data analysis to ensure consistency across experiments.
• Comprehensive Probe Coverage: Based on CATMA v2, the array uses 24,576 gene-specific sequence tags (GSTs) of 150–500 bp representing the majority of predicted Arabidopsis thaliana genes and including probes tiling chloroplastic and mitochondrial genomes.

Scientific Applications:

• Gene expression profiling: Enable comparative expression analyses across tissues, developmental stages, mutants, and environmental conditions.
• Functional genomics: Support inference of gene function and regulatory relationships from transcriptome patterns.
• Systems biology: Provide standardized datasets suitable for network reconstruction and integrative modeling.
• Mutation impact analysis: Facilitate assessment of transcriptomic effects of genetic variants and mutant alleles.
• Environmental response analysis: Allow investigation of plant transcriptional responses to diverse environmental scenarios.
• Meta-analysis integration: Permit cross-project integration and comparative meta-analyses within a standardized framework.

Methodology:

Data were processed using a uniform protocol from microarray printing to data analysis.