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. Author manuscript; available in PMC: 2014 Mar 4.
Published in final edited form as: Curr Opin Genet Dev. 2013 Mar 4;23(1):3–11. doi: 10.1016/j.gde.2013.01.004

Table 1.

microRNA profiling technologies

technologies advantages disadvantages Assay or platform/Vendor cost
quantitative reverse transcription PCR (qRT-PCR) Highly sensitivity and specificity. Low amount of RNA template and useful for absolute quantification Useful only for known miRs. Relative low number of samples that can be processed per day. TaqMan individual assays (ABI)
miRCURY LNA qPCR (Exiqon)
TaqMan OpenArray (ABI)
TaqMan TLDA microfluidics card (ABI)
Biomark HD system (Fluidigm)
SmartChip human microRNA (Wafergen)
miScript miRNA PCR array (SABiosciences/Qiagen)		 $$
miRNA microarray Relative low cost and high- throughput with respect to the number of samples that can be processed per day Lower specificity than qRT-PCR or RNA sequencing. Cannot be use for new miRs Geniom Biochip miRNA (CBC febit)
GeneChip miRNA array (Affymetrix)
GenoExplorer (Genosensor)
MicroRNA microarray (Agilent)
miRCURY LNA microRNA array (Exiqon)
NCode miRNA array (Invitrogen)
nCounter (Nanostring)
OneArray (Phalanx Biotech)
Sentrix array matrix and BeadChips (Illumina)
μParaFlo biochip array (LC Biosciences)		 $
RNA sequencing: high-throughput Useful for the detection of novel miRs. High sensitivity in discriminating between very similar miRs High cost. Large computational work for data analyses HiSeq 2000 and Genome Analyzer IIX (Illumina)
Solid (ABI)
GS FLX+ 454 sequencing (Roche)		 $$$
RNA sequencing: smaller scale Useful for the detection of novel miRs. High sensitivity in discriminating between very similar miRs High cost. Large computational work for data analyses Ion Torrent (Invitrogen)
MiSeq (Illumina)
GS Junior(454) (Roche)		 $$$