iCSDB: an integrated database of CRISPR screens.

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• CRISPR-Cas9 screening is vital for identifying functional target genes.
• Limited accessibility to public CRISPR screening data hinders research.
• Existing resources lack comprehensive, user-friendly integration of third-party experiments.

Purpose of the Study:

• To develop iCSDB, an integrated database for CRISPR screening experiments in human cell lines.
• To consolidate and standardize data from major CRISPR screening sources.
• To provide accessible tools for analyzing gene knockout efficiency and selecting cell lines.

Main Methods:

• Integrated data from the DepMap portal and BioGRID ORCS.
• Aggregated 1375 genome-wide CRISPR screens across 976 human cell lines.
• Removed batch effects and standardized screening scores for knockout efficiency.
• Incorporated clinical and molecular information for cell line selection.

Main Results:

• iCSDB contains 1375 genome-wide screens from 976 human cell lines, covering diverse tissues and cancer types.
• Standardized screening scores enable reliable comparison of knockout efficiency.
• Integrated clinical and molecular data facilitate cell line selection.
• Interactive tools allow detailed examination of gene and guide RNA level results.

Conclusions:

• iCSDB provides a centralized, user-friendly resource for CRISPR screening data.
• The database facilitates functional genomics research by improving data accessibility and analysis.
• iCSDB supports the selection of relevant cell lines and analysis of gene knockout efficiency.