Generation of a pooled shRNA library for functional genomics screens.

Dimitrios Papadopoulos, Carsten Patrick Ade, Martin Eilers

STAR protocols 2022 Mar 18

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Here, we detail a protocol for the generation of pooled short hairpin RNA (shRNA) libraries. We cover the design of optimized miR-E backbone shRNAs, cloning into a Tet-on vector system, and transformation of competent bacteria. We also describe library quality check by next-generation sequencing, and finally the production of lentiviruses. This protocol will generate high-quality inducible libraries suitable for both genome-wide and targeted functional genomics screens, allowing the high-throughput interrogation of protein depletion effects in the cell system of choice. For complete details on the use and execution of this protocol, please refer to Papadopoulos et al. (2022). © 2022 The Author(s).

Citation

Dimitrios Papadopoulos, Carsten Patrick Ade, Martin Eilers. Generation of a pooled shRNA library for functional genomics screens. STAR protocols. 2022 Mar 18;3(1):101183