Hello Experts, How do we decide time points of RNA extraction after giving drug to the cell lines for checking the gene expression profile in a microarray?
That will depend on the drug and the question you are asking. Are you attempting to link expression to a specific biological phenotype? If so, what is the phenotype and at what time point is it manifested?
That will depend on the drug and the question you are asking. Are you attempting to link expression to a specific biological phenotype? If so, what is the phenotype and at what time point is it manifested?
I agree with Adam. Do you know if there is any specific signaling pathway (eg. target gene expression or protein post-translational modifications) affected by the drug? You can do a time point study and measure the changes by RT-PCR or western blotting in order to determine the best time point to extract RNA. You might want to measure cell viability too to check if the dosage you used is toxic to the cells and at what time point significant cell death is induced.
If you want to see direct targets of the drug, use the earliest timepoint when you see any phenotypic change. A phenotypic change can be any kind of signal, including up- or down-regulation of a known target.
I am sorry to say this, but question is too vague. Can you please elaborate ? your purpose of drug administration, nature of cell lines , etc etc.........we may find a solution
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