How far are we from the era of big data in transcriptomics? Lessons from the bacterial data in GEO.

ABSTRACT: The Gene Expression Omnibus (GEO) is the largest functional genomics repository, including ~5 million entries related to the main transcriptomic technologies: microarrays and RNA-seq. This amount of data has the potential to be reused in large-scale meta-analysis, such as those in bacterial systems biology, where the landscape of biological conditions is wider and more diverse than any individual experiment alone. Notwithstanding the accelerated growth in RNA-seq experiments, microarray still accounts for ~48% of bacterial transcriptomic entries in GEO, highlighting the need to revalue this data. Therefore, in this work, we assess the current state of bacterial microarray and RNA-seq data and metadata. We report diverse inconsistencies in both the GEO metadata documentation and community u

SUBMITTER: Escobedo-Munoz AS 

PROVIDER: S-EPMC12548026 | biostudies-literature | 2025 Aug

REPOSITORIES: biostudies-literature