CRISPRepi

CRISPRepi consolidates extensive sequencing data from RNA-seq, ChIP-seq, Bisulfite-seq, and ATAC-seq datasets to enable analysis of CRISPR-based epigenome editing outcomes and assessment of off-target effects.

Key Features:

• Multi-omic data integration: Consolidates 671 curated RNA-seq, ChIP-seq, Bisulfite-seq, and ATAC-seq datasets from 2277 samples across six species.
• sgRNA and target gene curation: Contains 5962 sgRNAs associated with 283 target genes.
• Cell type and editing system coverage: Covers 87 cell types manipulated by 74 epigenome editing systems.
• Editing outcome analysis: Analyzes gene expression changes pre- and post-editing along with multi-omic epigenetic landscape details.
• Off-target effect assessment: Evaluates off-target effects across diverse CRISPR-based epigenome editing systems.
• Cell/tissue-specific sgRNA investigation: Supports investigation of editing potentials for newly designed sgRNA sequences in a cell/tissue-specific context.

Scientific Applications:

• Editing system evaluation: Enables comparison of precision among different epigenome editing systems.
• Optimal sgRNA design: Facilitates selection of optimal sgRNAs for functional studies across multiple organisms.
• Epigenetic landscape analysis: Supports analysis of multi-omic epigenetic changes resulting from CRISPR-based epigenome editing.
• Gene regulation studies: Aids in designing tunable and reversible gene regulation strategies without altering DNA sequences.

Methodology:

CRISPRepi analyzes gene expression changes pre- and post-editing and examines multi-omic epigenetic landscape details; the specific computational algorithms are not explicitly stated in the sources.