The gels may be run on either agarose or denaturing polyacrylamide, the latter being preferable for smaller fragments of RNA. Unlike in the Southern blot, formaldehyde is added to the gel and acts as a denaturant to agarose. For polyacrylamide, urea is the denaturant.
As in the Southern blot, the hybridization probe may be made from DNA or RNA.
A variant of the procedure known as the reverse northern blot is occasionally used. In this procedure, the substrate nucleic acid (that is affixed to the membrane) is a collection of isolated DNA fragments, and the probe is RNA extracted from a tissue and radioactively labelled.
The use of DNA microarrays that have come into widespread use in the late 1990s and early 2000s is more akin to the reverse procedure, in that they involve the use of isolated DNA fragments affixed to a substrate, and hybridization with a probe made from cellular RNA. Thus the reverse procedure, though originally uncommon, enabled northern analysis to evolve into gene expression profiling, in which many (possibly all) of the genes in an organism may have their expression monitored.