Performing target validation well
This blogpost describes issues encountered in target validation and how to safeguard against poor reproducibility in RNAi experiments.
5 factors to consider in multi-gene targeting RNAi screens
Effective functional genomic screening depends on a variety of factors that need to be simultaneously addressed to obtain meaningful results. A recent Cell Reports paper demonstrates this by taking a holistic approach to siRNA screening with the use of multi-isoform/multi-gene targeting to address redundant paralogs and pathways in cancer cells.
Disrupting lncRNA function with siPOOLs (RNAi), antisense oligos and CRISPR
This blogpost covers methods used in the disruption of lncRNA function. Specifically focusing on RNA interference (with siPOOLs), antisense oligos, and CRISPR approaches. Challenges faced with these approaches are addressed.
"Phenoville" - RNAi & CRISPR Screening Strategies
Comparing RNAi and CRISPR screening strategies in host-virus interactions. RNAi offers broader insights, CRISPR specificity.
CRISPR/Cas9 Screening - The “Copy-Number Effect”
Exploring the `copy number effect` in CRISPR/Cas9 screens for essential genes in cancer cell lines. The phenomenon reveals a challenging source of false positives and negatives, prompting the development of computational methods for correction and emphasizing the need for cautious interpretation and complementary validation techniques.
Unexpected Mutations after CRISPR in vivo editing - post-commentary
Delving into concerns surrounding a Nature Commentary on CRISPR-edited mice, including study size, control choice, Cas9 delivery, and variant validation. Critics emphasize the need for rigorous controls and updated databases to assess off-target effects accurately.
How reproducible are CRISPR screens?
Exploring the reproducibility of CRISPR screens compared to RNAi screens. While CRISPR gRNAs show more consistent gene inhibition, overlap in top hits between CRISPR screens varies, cautioning against overestimating reliability solely based on assay reproducibility.
CRISPR - what can go wrong and how to deal with it
CRISPR's potential pitfalls highlighted: absent phenotypes, inefficient editing, and unexpected results, with strategies for effective management.
Knocking out the phenotype
Explore the implications of gene knockout on phenotype. Learn from recent research indicating a lack of phenotypic response when knocking out klf2a, contrasting with knockdown outcomes.
Genetic compensation
Discover how genetic compensation alters gene knockout outcomes. Learn from research by Rossi et al. on phenotypic mitigation post gene knockout.
