We are planning to do a miRNA profiling to distinguish between two disease conditions with similar and closely associated clinical conditions. Which method of profiling is suitable such as qPCR based or NGS.
Dr. Ramaswamy, that depends on your purpose whether you wish to identify all miRNA from the tissue or the selected candidate miRNA. For global profiling NGS is best suitable method while for selected ones qPCR would be better.
I agree that would depend on your purpose but I would also use RT-qPCR to validate the NGS data.
For microRNA profiling I would not select qPCR, you could go for NGS or array, and then use the qPCR to validate the most important ones.
If you are planning to do a miRNA profiling to distinguish between two disease conditions with similar and closely associated clinical conditions.Then NGS is the best method. Because you are not having specific targeted miRNAs. You want to screen microRNAs which may be common in both the diseases or you want to check the differential expression of microRNAs among both the diseases. If you do profiling through NGS, You dont need to go for qRT-PCR. Through NGS you also do the expression by using DEGseq algorithm and in this analysis results you will get definitely few numbers og highly differential expressed microRNAs and you can validate them by nothern blotting or qRT-PCR. So it will validated study as well a broad and novel spectrum of microRNAs can be generated. I would recommend you should go for tissue specific NGS profiling microRNAs because it will give you specific data for you both the diseases.
You can also check my publication for this I hope that will help you a lot
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0139359
As mentioned above it depends on your aim. For known microRNAs, you can use microRNA array. If your aim is to identify novel microRNAs then you have to go with small RNA Seq. I would use NGS, you can profile both known and novel microRNA.
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