IPdb

IPdb provides a curated database of PIWI-bound piRNA sequences derived from immunoprecipitation RNA-seq experiments to support analysis of piRNA biogenesis, processing, and function.

Key Features:

• Dataset size: Comprises 18,821,815 sequences derived from RNA-seq experiments following immunoprecipitation.
• Source material: Sequences originate from small RNA libraries obtained after PIWI protein immunoprecipitation (piRNA-IP).
• Species and proteins: Includes small RNAs associated with mouse PIWI proteins MILI, MIWI, and MIWI2.
• Sequence characteristics: Focuses on small non-coding RNAs in the ~21–35 nucleotide size range typical of piRNAs.
• Curation criterion: Retains sequences exclusively based on PIWI binding to represent bona fide piRNAs.
• Biochemical features: Captures piRNA-relevant properties including 5' uridine enrichment and 3' methylation associated with stability.

Scientific Applications:

• piRNA biogenesis and processing: Enables analysis of piRNA maturation pathways and sequence features relevant to biogenesis.
• Functional studies: Supports investigation of piRNA roles in defending genomic integrity against transposable elements.
• Somatic and germline comparisons: Facilitates studies of piRNA presence, activity, and pleiotropic roles in somatic cells versus germline.
• Developmental and cell-type analyses: Allows comparative analyses of piRNA repertoires across cell types and developmental stages.

Methodology:

Build set from 18,821,815 sequences obtained from RNA-seq experiments following PIWI immunoprecipitation and curated to retain sequences bound to mouse PIWI proteins (MILI, MIWI, MIWI2).