Table 1.

Summary of current profiling methods for miRNAs

	Methods for profiling miRNA expression
Small RNA cloning and sequencing	The original small RNA discovery approach. Require 3′ and 5′ ligation and PCR amplification. With the application of next-generation sequencing and genome-wide bioinformatic annotation, this method becomes one of the most powerful tools to profile small RNA expression, including miRNAs. Suitable for large-scale high-throughput profiling. Absolute abundance of miRNAs can be referred by the cloning frequency.
MiRNA microarray	Similar to microarray for mRNAs, the expression of individual miRNAs can be compared across many different samples. Many commercial platforms are available with the requirement of <1 μg total RNA. Suitable for large-scale high-throughput profiling of miRNAs in many different samples such as clinical samples.
Real-time PCR-based profiling	Highly sensitive for the detection of changes in individual miRNA expression. Suitable for quantitative study of the expression of a small number of miRNAs. Multiplex approaches are also developed to profile all known miRNAs (similar to the microarray approach but with higher sensitivity).
In situ hybridization	Require LNA-modified probes for enhanced affinity and specificity to miRNAs. Accurately monitor individual miRNA expression in a spatiotemporally specific manner. Provide the most accurate profiling of a single miRNA in cell lineages or clinical samples.
Northern blotting	Classic method to measure the expression of individual miRNA. Often detect both mature miRNA and pre-miRNA at the same time. But require relatively large amount of total RNA input. Still a method of choice to validate the existence of novel miRNAs (small RNA cloning and sequencing can also be applied).

Technical features and potential applications are listed in each column