Saturday, November 21, 2009

Running lots of PCRs at once

We have two projects now where we want/need to quantify lots of genes in each sample. For one we have the microarray experiments that need PCR validation, and then we are characterizing renal damage in some models we haven't used before. In total this is over 200 samples, and we are interested in at least 20 genes.

Of course we could just run our usual RT-RTPCRs in triplicate using 20µl reactions, but not only is that an enormous amount of pipetting, it is also horrendously expensive.

We were going to use the SuperArray, which we tried in a previous project, but it only simplifies the plating, you still have to pipett your reaction mix and samples into each of the wells. Then we found the Taqman Low Density Array, where you basically just pipett each sample once and it is run on (in our case) 48 different genes in a specialized PCR-machine. So the PCR machine is a problem, but luckily there was one available at the central lab for genomics that we could use.

I am looking forward to trying this new thing, using 1/10th the reagents and 1/48th the pipetting for half the prize. On the other hand, when it is this easy it really puts PCR into the realm of too simple to be called science. It still has to be done though.

Now I am just hoping for the same kind of automation in protein quantification. I have some hopes for this thing called MRM-MS, and it will soon be available at the central lab for proteomics just around the corner from our lab. More on that to come.