tsRBase

tsRBase catalogs expression and functional data of tRNA-derived small RNAs (tsRNAs) across 20 species by integrating >14,000 small RNA-seq datasets and evidence from CLIP/RIP-seq, CLASH, and CLEAR-CLIP to support study of their regulatory roles.

Key Features:

• Extensive data collection: Aggregates over 14,000 publicly available small RNA-seq datasets annotating 121,942 tsRNAs across 20 species including bacteria, fungi, plants, and animals.
• Expression patterns: Catalogs tsRNA expression across tissues, cell lines, treatments, and genetic backgrounds to profile condition-specific abundance.
• Functional evidence: Integrates experimentally validated tsRNAs from published literature, protein-binding tsRNAs identified by CLIP/RIP-seq, and tsRNA targets determined by CLASH and CLEAR-CLIP.
• Spatiotemporal expression: Records spatiotemporal expression patterns to represent dynamic regulatory potential of tsRNAs across biological contexts.

Scientific Applications:

• Regulatory mechanism studies: Supports investigation of tsRNA-mediated modulation of gene expression across species and conditions.
• Interaction and target identification: Enables mapping of protein-binding tsRNAs and their targets using integrated CLIP/RIP-seq and CLASH/CLEAR-CLIP evidence.
• Disease and therapeutic research: Facilitates exploration of tsRNA involvement in disease pathogenesis and assessment of potential therapeutic implications.
• Hypothesis generation and experimental design: Provides comprehensive datasets and functional annotations to inform experimental planning and hypothesis development.

Methodology:

Compilation and analysis of high-throughput small RNA-seq datasets and integration of CLIP/RIP-seq, CLASH, and CLEAR-CLIP data, together with curation of experimentally validated tsRNAs from published literature.