Family: Bioinformatics Analysis Services
Cellecta Inc. provides comprehensive analysis services for functional genetic screens utilizing pooled lentiviral CRISPR and shRNA libraries sequenced at Cellecta. Get details on Cellecta's service for genomic DNA isolation, sequencing, and basic guide frequency reporting, at Sequencing Service for Samples from Genetic Screens.
In addition to these core steps, Cellecta's Functional Genetic Screening Bioinformatics Analysis pipeline integrates computational tools like MAGeCK, DrugZ, and custom in-house developed scripts to assess gene enrichment or depletion, identifying essential genes, gene-drug interactions, and key pathways related to specific phenotypes.The information below describes further downstream bioinformatics analysis offerings, i.e. the last step of the workflow illustrated in Fig. 1.
Fig. 1: Overview of Genetic Screen Analysis Services
The CRISPR Analysis workflow (Fig. 2) that results in our basic report includes the Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) essential data quality and control analyses, providing information on
Fig. 2: CRISPR Analysis Workflow
For more in-depth analysis, we have developed several bioinformatics modules to support the analysis of various CRISPR screening projects, an advanced report, including:
MAGeCK Analysis (Default Option)
MAGeCK (Model-based Analysis of Genome-Wide CRISP-Cas9 Knockout) analysis integrates both RRA (Robust Rank Aggregation) and MLE (Maximum Likelihood Estimation) methods to consistently identify genes with significant enrichment or depletion, offering deep insights into gene function and the pathways involved in your experiments.
RRA andMLE
RRA is the preferred method in MAGeCK analysis due to its ability to aggregate sgRNA ranks, and provide robust gene ranking. It effectively handles variability across guides and reduces noise, making it highly reliable for large-scale CRISPR screens. MLE, on the other hand, is ideal for studies involving different isolines, offering precise, quantitative estimates of gene effects in diverse genetic backgrounds.
Additional MAGeCK features
Our analysis includes RRA Comparison Summaries, Volcano Plots of Selected Genes, and MLE Comparison Summaries, offering a detailed distribution of gene beta scores and identification of positively and negatively selected genes. Pathway enrichment analysis (Gene Set Enrichment Analysis (GSEA), KEGG, Gene Ontology (GO), Reactome) is also available.
DrugZ (Drug Screening Analysis) - by request only
DrugZ is tailored for CRISPR screens involving drug treatments, detecting genes that influence drug sensitivity or resistance. It offers a focused approach to identifying drug-gene interactions to advance drug discovery and precision medicine.
CRISPR Tiling Analysis
Cellecta designs CRISPR tiling libraries and provides bioinformatics analysis for screens using them. This analysis technique identifies functional domains within proteins, and critical elements in annotated genes or enhancers by targeting multiple gene segments. Analysis of tiling screens helps uncover "drop out" regions, revealing essential genomic elements and key protein domains (Fig. 3).
Fig. 3 CRISPR tiling analysis data
Ready to get new insights from your functional screening data? Let us know what you need on the form to request a quote now or contact us at info@cellecta.com for more information. Our expert team is happy to assist you superpower your research.
