An integrated pipeline for mammalian genetic screening

Area of Science:

• Genomics and Molecular Biology
• Mammalian Cell Biology
• Bioinformatics

Background:

• Recent advances in genome editing, next-generation sequencing (NGS), and scalable cloning enable large-scale, precise genetic screens.
• A need exists for a unified, user-friendly pipeline to conduct systematic mammalian genetic screening.
• Existing technologies require integration into a cohesive workflow for efficient cell state engineering.

Purpose of the Study:

• To develop a comprehensive and user-friendly pipeline for systematic mammalian genetic screening.
• To create novel algorithms for target identification and a specialized cloning tool (MegaGate).
• To enable versatile engineering of mammalian cell lines for various applications.

Main Methods:

• Development of unique algorithms for target identification.
• Creation of a toxin-less Gateway cloning tool named MegaGate for library construction.
• Integration of MegaGate with existing genetic perturbation methods and NGS-coupled readouts.
• Implementation of the STAMPScreen pipeline for sequencing-based target ascertainment and modular perturbation screening.

Main Results:

• Successful development of the STAMPScreen integrated pipeline.
• Demonstration of MegaGate's utility in library cloning for mammalian systems.
• Validation of the pipeline's capability for versatile cell state engineering.
• Establishment of a scalable and precise method for genetic screening.

Conclusions:

• The STAMPScreen pipeline offers a simplified yet comprehensive approach to mammalian genetic screening.
• The developed tools and integrated pipeline facilitate precise cell engineering and target identification.
• STAMPScreen is applicable to a wide range of cell state engineering applications, advancing genetic research.