Table 2

Methods of transcriptome analysis2

Name of technologyTechniqueAdvantagesDisadvantages
Next-generation sequencing; RNA seqRNA is fragmented, sequenced and compared against a reference sequence.More comprehensive and good coverage.
Allows quantification of transcripts and broad discovery, no prior knowledge needed and alternative splicing isoforms viewable.
Huge amount of information generated.
MicroarraySample hybridises with probes for specific transcripts fixed to array and determines if sequence present in sample.Cheap, comprehensive coverage and allows quantification of transcripts.Not sensitive—unable to detect transcripts that are not in the probe set.
Real-time quantitative PCRAmplification of targeted RNA sequencesSensitive.
Allows quantification of transcripts.
Useful for validation of other methods.
Limited scope and coverage.