I am looking to create stable cell lines HCT116 for gene silencing . I am not satisfied with the siRNA experiments ( not great transfection efficiency so far and
SiRNA mediated transfections are often regarded as better compared to Stable sh clones, as it may block different variants of the transcript.
If you want to make effective knockouts go for CRISPR/Cas9.
For SiRNA you can use RNAiMAX for better transfection efficiency.
I agree, stable transfection with shRNA should offer the features requested in your experimental setting.
(For ref. see e.g.: Lambeth LS, Smith CA. Short hairpin RNA-mediated gene silencing. Methods Mol Biol. 2013;942:205-32. doi: 10.1007/978-1-62703-119-6_12.).
Dear Eirini, gene silencing using siRNAs most of the time needs huge optimizations and repetitions to perform. Low cell viability and low transfection efficiency are the main culprits but both can be optimized. If you are not using fluorescent labeled transfection control so I will insist to do so, as you would be more sure that is there any problem in your transfection media or it is something else. In addition, purchase that siRNA which possess highest target specificity and induces almost zero level cell stress or any innate immune response. "Silencer-Stealth siRNA" are the best in this regard being more stable (upto 72 hours) and their biology limits the off-target effects more effectively. Alternatively, if you are not satisfied you can jump over to shRNAs and see. But, I would suggest here to engage into some serious optimizations and you will succeed.
You can get further help and understandings regarding siRNA optimization strategies through my previously given answer in the link following;
Just check it,
https://www.researchgate.net/post/How_to_increase_KD_efficiency
Best Wishes...
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