miRNA expression profiling - (Dec/07/2012 )
Recently i am involved in conducting a genetic study on miRNA expression analysis. Since i am new to this field i would like to gather the basic information on the following
List of method available to peform miRNA expression profiling
How to choose miRNA for custom profiling
My study design is to check the miRNA expression pattern between two population exposed to different environmental factors.
1. miRNA microarray
2. deep sequencing
You have to look into the literature to find relevant microRNA to include.
I've used Agilent Human miRNA microarrays. This one is increasingly becoming popular although people nowadays are not afraid of going for sequencing (miRNAseq) instead of microarrays.
Advantages: Fairly Low-cost and high-throughput
Disadvantages: Can not detect novel miRNAs,
As an alternative to microarray profiling, people are using qRT-PCR profiling such as TaqMan® Low Density Array MicroRNA Panels.
Advantages: Sensitive and specific, can be used for absolute quantification
Disadvantages: Can not detect novel miRNAs, Low throughput compared to microarray and sequencing
MIRNAseq is becoming wide-spread with the costs for high-throughput next generation sequencing becoming lower and lower each year.
Advantages: Can detect novel miRNAs, can distinguish between closely related sequences with great accuracy
Disadvantages: Cost is still high in certain parts of world, high computational work needed,
See some references here and here.
Selection of miRNAs for custom profiling largely depends on, as pcrman suggested, the published literature and how each miRNAs your identify are related to your experiment and the questions that you want to answer through this experiment,
Check out our article in PLOS One about free QPCR assay design for miRNA or siRNA detection.