Similar seed effects in independent siRNA screens
A 2013 study on Parkin translocation used genome-wide siRNA libraries from Ambion (single Silencer Select siRNAs) and Dharmacon (pools of 4 siGENOME siRNAs).
Clearly compensating
Genetic compensation by transcriptional adaptation is a process whereby knocking out a gene (e.g by CRISPR or TALEN) results in the deregulation of genes that make up for the loss of gene function.
Pooling only 4 siRNAs increases off-target effects
Low-complexity pools (with 4 siRNAs per gene) should thus lead to overall stronger off-target effects than single siRNAs.
Little correlation between Dharmacon siGENOME and ON-TARGETplus reagents
Analysis reveals little correlation between Dharmacon siGENOME and ON-TARGETplus, highlighting the complexity of validating RNAi screen hits.
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.
siRNA vs shRNA - applications and off-targeting
Exploring siRNA vs shRNA for gene silencing: applications, off-target effects, and why choosing the right RNAi method matters for your research.
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.
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.
