Editing Northern blot (section)

===Gels===
[[Image:RNA agarose gel.svg|thumb|RNA run on a formaldehyde agarose gel to highlight the 28S (top band) and 18S (lower band) ribosomal subunits.]]
The RNA samples are most commonly separated on [[agarose]] gels containing [[formaldehyde]] as a denaturing agent for the RNA to limit secondary structure.<ref name="Streit2009" /><ref name=Yamanka1997>{{cite journal | last1 = Yamanaka | first1 = S. | last2 = Poksay | first2 = K. S. | last3 = Arnold | first3 = K. S. | last4 = Innerarity | first4 = T. L. | year = 1997 | title = A novel translational repressor mRNA is edited extensively in livers containing tumors caused by the transgene expression of the apoB mRNA-editing enzyme | journal = Genes Dev. | volume = 11 | issue = 3| pages = 321–333 | doi = 10.1101/gad.11.3.321 | pmid = 9030685 | doi-access = free }}</ref>  The gels can be stained with [[ethidium bromide]] (EtBr) and viewed under UV light to observe the quality and quantity of RNA before blotting.<ref name="Streit2009" />  [[Polyacrylamide]] gel electrophoresis with [[urea]] can also be used in RNA separation but it is most commonly used for fragmented RNA or microRNAs.<ref name=Valoczi2004>Valoczi, A., Hornyik, C., Varga, N., Burgyan, J., Kauppinen, S., Havelda, Z. (2004) Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nuc. Acids Research. 32: e175.</ref>  An RNA ladder is often run alongside the samples on an electrophoresis gel to observe the size of fragments obtained but in total RNA samples the ribosomal subunits can act as size markers.<ref name="Streit2009" />    Since the large ribosomal subunit is 28S (approximately 5kb) and the small ribosomal subunit is 18S (approximately 2kb) two prominent bands appear on the gel, the larger at close to twice the intensity of the smaller.<ref name="Streit2009" /><ref name=Gortner1996>{{cite journal | last1 = Gortner | first1 = G. | last2 = Pfenninger | first2 = M. | last3 = Kahl | first3 = G. | last4 = Weising | first4 = K. | year = 1996 | title = Northern blot analysis of simple repetitive sequence transcription in plants | journal = Electrophoresis | volume = 17 | issue = 7| pages = 1183–1189 | doi = 10.1002/elps.1150170702 | pmid = 8855401 | s2cid = 36857667 }}</ref>