Feature Nuclease
Protection Assays
Northern Blotting RT-PCR In Situ
Relative and Absolute Quantitation YesYesYesYes
Detection Limit (Copies of mRNA)4,000-5,00010,0001 (theoretical) Medium
Level of Optimization Required MediumMediumHighHigh
Sample Size 100 µg max 30 µg maxNot critical Tissue sections
Detect Multiple Transcripts Yes, in same tube Yes, generally requires stripping and reprobing Yes, in same tube No
Localizes mRNA Expression within Tissues/Cells NoNoNoYes
Mapping Studies YesNoNoNo
Resolve Comigrating mRNAs YesNoYesNo
Sizing mRNAs NoYesNoNo
Detection of Alternatively Spliced Transcripts NoYesNoNo
Distinguish Between Members of Multi-Gene Families YesOnly if they are different sizes Only if they are characterized No
Tolerates Partially Degraded RNA YesNoYesYes
  • Can use up to 100 µg of sample RNA
  • Ease of multiprobing
  • Tolerates partially degraded RNA
  • RNA undergoes minimal processing
  • Technique can be easily evaluated at various points in procedure
  • Most sensitive technique available
  • Localized mRNA within tissue
  • Tolerates partially degraded RNA