crisprSQL

crisprSQL provides a SQL-based database of CRISPR/Cas9 off-target cleavage data, aggregating base-pair-resolved cleavage frequency distributions and epigenetic annotations from human and rodent cell lines to support analysis of off-target effects, guide RNA design, and algorithm development.

Key Features:

• SQL-based Database: crisprSQL stores curated CRISPR/Cas9 cleavage data and annotations in an SQL-based schema.
• Extensive Data Collection: The dataset comprises cleavage data from 144 guide RNAs across 25,632 guide-target pairs derived from human and rodent cell lines.
• Epigenetic Annotation: Entries include epigenetic annotations and base-pair-resolved cleavage frequency distributions linked to gene names and epigenetic markers.
• Attached Gene IDs: Records include attached gene IDs to enable integration with transcriptomic datasets.
• Curated Dataset for Algorithm Development: The curated dataset supports development and benchmarking of computational algorithms predicting off-target cleavage events.

Scientific Applications:

• Cleavage Profiling: High-resolution cleavage frequency distributions enable profiling of CRISPR/Cas9 activity across genomic regions.
• Gene Editing Safety Analysis: Comprehensive off-target profiles support quantification and assessment of gene editing safety.
• Transcriptomics Research: Attached gene IDs and cleavage data facilitate integration with transcriptomic analyses.
• Guide RNA Design and Experiment Planning: Aggregated off-target data inform guide RNA selection and experimental planning to anticipate potential off-target effects.
• Development of Computational Algorithms: The curated dataset provides empirical data for training and validating off-target prediction algorithms.

Methodology:

Data are stored in an SQL-based database and annotated with base-pair-resolved cleavage frequency distributions and epigenetic information.