TTDB: a comprehensive Transcriptome Turnover Database for exploring mRNA stability

The regulation of messenger mRNA turnover is a critical cellular process that dictates gene expression levels. High-throughput sequencing technologies have enabled the measurement of mRNA decay rates on a transcriptome-wide scale. However, this vast amount of data is dispersed across numerous publications, and it is cumbersome to harmonize and compare. To address this, we have developed the Transcriptome Turnover Database (TTDB), a centralized and comprehensive resource for genome-wide mRNA stability data. TTDB integrates 198 high-throughput datasets from 57 publications, with an average 12 544 genes per dataset, across five species: human, mouse, zebrafish, fruit fly, and yeast. The database not only provides experimentally determined and computationally standardized mRNA half-lives and decay rates, but also offers precomputed annotations for each transcript, including GC content, minimum free energy of mRNA secondary structure, and counts of regulatory elements like upstream AUGs and AU-rich elements. The user-friendly web interface allows users to intuitively browse, search, visualize, and download data by study, sample, or gene. TTDB is publicly accessible at https://sysbio.gzzoc.com/ttdb/index.html.