Table 1 Advantages and limitations of each platform

NanoString

(1) RNAs are directly measured without amplification or cloning; (2) Digital readout generates less background noise; and (3) Allows high dynamic range of expressions.

(1) Only a limited number of probes are available to measure isoform or gene expression; and (2) Sophisticated custom probe design is often needed.

RNA-seq

(1) No requirement of gene annotations; (2) Capable of detecting novel splicing isoforms; (3) Allows high dynamic range of expressions; and (4) Provides transcriptome-wide expression profiling.

(1) Transcript specific bias/ 3’-end bias; and (2) Various sampling biases as a result of library preparation protocols.

Exon-array

(1) Provides transcriptome-wide expression profiling; and (2) Capable of measuring expressions at exons and exon-junctions.

(1) Limited dynamic range; (2) Requires a higher amount of molecules in RNA preparation; and (3) Depends on existing genome annotation.

RT-qPCR

(1) High dynamic range of expressions; (2) Less biased results; and (3) much cheaper in comparison to RNA-seq and Microarray on a small-scale study.

(1) Only a limited number of transcripts can be measured; and (2) Custom primer designs are often needed.