Which methods are proper to study gene silencing when we give the LncRNA or miRNA to the cell culture diseases model. For example in hippocampal neuron cell model in alzheimer disease which pathways should we study to analysis gene silencing by non coding RNA? (JAK/STAT or Wnt pathways?)
Dear Mesut Karahan
If I am not understanding wrong, then you are saying that you want to study the genes and associated pathways which get silenced on miRNA overexpression.
Definitely miRNA either cause transcription inhibition or repression of translation. So, when we overexpressed miRNA, a huge panel of genes of different pathway get downregulates as a action of miRNA, in many times upregulates also may be due to some kind indirect action.
Now to check the gene silenced, you can go start qPCR and western blotting. Genes can be predicted using different target prediction tools.
The pathway, you can decide based on impact of that pathway in ur AD model.
In advance indepth analysis (say in our cancer study), we have done Nanostring Pancancer panel analysis which consist 770 genes panel which belong to 14 different pathway. Nanostring is very new method to study differential expression of genes.
Even you can think of RNA sequencing, Microarray...
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