| Amount of starting RNA required | Sensitivity of test | Analytic requirements | Information obtained from the test | Number of targets | Relative cost | Advantages | Disadvantages | |
| Northern blot | High | Low | Low | Presence and size of RNA of interest | Few | Low | Straightforward | Risk of RNA degradation |
| Radioactivity use | ||||||||
| Lower sensitivity | ||||||||
| Higher starting quantity of RNA | ||||||||
| Ribonuclease protection assay | High | Moderate | Low | Presence and size of RNA of interest | Few | Low | Higher specificity for the gene | Complex protocol |
| Better sensitivity | Radioactivity use | |||||||
| In-situ hybridization | High | Low to moderate | Low | Presence and spatial localization of RNA of interest | Few | Low | Spatial localization in a tissue section or cell | Low sensitivity |
| Qualitative, not quantitative | ||||||||
| Spotted cDNA arrays | Moderate | Moderate to high | Moderate to high | Relative gene expression between two conditions | Several hundred | Moderate | Simultaneous detection of hundreds of genes | Limited reproducibility |
| Direct comparison of two samples | ||||||||
| Oligonucleotide arrays | Low to moderate | Moderate to high | Moderate to high | Relative gene expression | Thousands | Moderate | Simultaneous detection of thousands of genes | Analysis limited to known genes |
| Higher resolution than older methods | Decreased sensitivity for lowly expressed transcripts | |||||||
| RT-PCR | Low | High | Low to moderate | Relative gene expression | Few to several hundred | Low | Straightforward protocol | Needs careful primer selection |
| Higher sensitivity | ||||||||
| Transcriptome sequencing | Low to moderate | High | Very high | Digital counts of each RNA molecule (as measure of gene expression) with excellent dynamic range | Unlimited | High | Higher resolution than microarrays | High cost |
| Large dynamic range, can detect low abundance transcripts | Low throughput | |||||||
| Detects novel transcripts | Large storage space needed for data | |||||||
| Can identify polymorphisms within a sequence | Intensive computational analysis |
