A question about positive screening

Usually,we can find resistant genes by positive screening,but in this process,some sgRNA will deplete in drug treatment group but not in DMSO group ,How to explain this phenomenon?

Besides,If i want to find a gene which losts can enhance the effect of a drug by negative screening(Just like synthetic lethality).How do I determine the concentration of this drug during the screening process?IC50?Or a lower concentration?


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Fuchsia Kelpieover 4 years ago

In both positive and negative selection genome-scale screens, you will usually see both enrichment and depletion of sgRNAs, because some genes are involved in drug resistance and others are involved in synthetic lethality. Using the IC50 of the drug during the screening selection is ideal and allows you to see both enrichment and depletion.

Jade Wendigoover 4 years ago

i wonder how long did you calculate IC50 value after drug treatment? My personal understanding is 72 hour,but in some articles I found that they are calculating IC50 after dealing for 14 days。Is there any difference between the two methods?

Besides, if my goal was to identify genes that, when silenced, enhanced the response to a drug, Is IC20 or IC10 better?

Fuchsia Kelpieover 4 years ago

When we run drug dose curves, we usually do 72h treatment, which for most cancer drugs should be sufficient to determine the IC50, but there may be some drugs that will require shorter or longer treatment times. Even if you are trying to identify genes that enhance the response to a drug, you would still use the IC50 value to get the greatest shift between positive and negative controls.

Jade Wendigoover 4 years ago

Thank you very much.

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