CRISPRroots

CRISPRroots integrates RNA-seq and CRISPR-Cas9 edit data to distinguish differential gene expression caused by intended on-target edits from unintended off-target effects by combining transcriptomic and genomic variant information.

Key Features:

• Integration of Genomic and Transcriptomic Data: Combines CRISPR-Cas9-mediated edit information with RNA-seq data to assess on-target and potential off-target sites simultaneously.
• Assessment of Off-Target Effects: Leverages Cas9 and guide RNA binding properties together with gene expression changes and sequence variant comparisons to identify candidate off-target effects.
• Data-Driven Discovery: Applies data-driven analyses to public datasets to identify off-target candidates and re-evaluate previously published studies for undetected off-targets.
• Resource Efficiency: Focuses on integrated transcriptomic and variant evidence to reduce reliance on genome-wide sequencing for off-target detection.

Scientific Applications:

• Attribution of differential expression: Distinguishes whether observed gene expression changes arise from intended CRISPR-Cas9 edits or from unintended off-target modifications in studies of genomic variants and gene knockouts.
• Re-analysis of published datasets: Re-assesses published RNA-seq and editing datasets to uncover off-target effects missed in original analyses.

Methodology:

Analyzes Cas9 and guide RNA binding properties, compares gene expression profiles between edited and non-edited cells, and identifies sequence variants between cell populations.