Dear all,
My aim is investigating the effect of a plant extract on gene expression pattern in cancer cell lines based on RNA-seq.
How can I find the best RNA extraction time in which genes diffrentioally expressed with highest confidence.
All suggestions are welcomed
You need to do different exposure and collection time series to see which one responds the best and this could be a part of your project too.
Good luck
Dear Esmaeili, the best challenge time may be 2-4h. You need to take a positive control i.e. H2O2, LPS, TNF-alpha etc. and check whether your gene of interest express in challenge time. Also you need to perform viability Studies with the test concentration of your plant extracts at different exposure times. Hope it helps.
Your need to study your plant extract at different exposure times
Dear Dr Panwar,
Thank you for your answer.
So the procedure is:
1- determining the cytotoxic concentration of plant extract.
2- extraction RNA at different exposure times
3- studying the expression of positive controls
Is it right?
I would be really grateful if you could explaine alittle about each step .
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