Ribo-depletion in RNA-Seq – Which ribosomal RNA depletion method works best?
This blogpost is focussed on ribosomal RNA (rRNA) depletion methods frequently applied to improve and economize RNA-Seq experiments.
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.
Understanding Gene Networks with Combinatorial Gene Knockdown
Combinatorial gene knockdown with siPOOLs unveils complex gene networks, offering a deeper understanding of gene functions and interactions
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.
RNA affinity purification: Tips for optimizing
Optimize RNA Affinity Purification: Key strategies for effective isolation, analysis, and insights into RNA interactions.