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RT-PCR vs Northern

Eric C. Anderson e-anderson at ski.mskcc.org
Sat Dec 2 15:46:54 EST 1995

In article <Stephen_Lasky-0212950741390001 at cis-ts1-slip1.cis.brown.edu>,
Stephen_Lasky at brown.edu (Stephen R. Lasky) wrote:

> In article <49l20s$bq at mark.ucdavis.edu>, ez008413 at bullwinkle.ucdavis.edu
> (Gabriel Romero) wrote:
> > I'm about to start gene expression studies at the transcription level but 
> > I have not decided between RT-PCR and Northern analysis as the method to 
> > use.  I only need to have a yes or no answer for expression initially and 
> > then have some idea on the level of expression.  How do the methods 
> > compare in terms of ease/difficulty in running the experiments, and in 
> > terms of amount and quality of information?
> > 
> > Thanks for any advice.
> > 
> > 
> > Gabby Romero
> RT-PCR is much more sensitive, faster, requires less RNA, and is easy to
> do.  It is, however, more difficult to quantitate.  You also need to be
> able to design good primers (which is usually not too much of a problem).
i agree.  i'm currently running northerns for a number (about 120) of
candidate genes discovered via RT-PCR because the quantitation is much
easier to do with a northern for this number of clones.  so if all you
need is a yes or no answer, RT-PCR will likely be quicker and easier to do
for the aforementioned reasons.  however, if you end up having a bunch of
them to quantitate, the amount of troubleshooting involved in quantitative
RT-PCR might be more hassle than it's worth.

good luck,


Eric C. Anderson
Cell Biology and Genetics
Memorial Sloan-Kettering Cancer Center
Sloan-Kettering Institute
1275 York Ave., Box 470
New York, NY  10028
Phone: (212)639-2977
Fax:   (212)717-3298
e-anderson at ski.mskcc.org

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