High throughput RNA extractions - best methods/kits?

[JeremyDay]

Hi All,

We have a large number of RNA samples coming (most likely in Trizol) this year. I'd like to streamline and get some consistency by deciding on a product that gives good quality (260/280, 260/230, RIN), yields, easier than columns, and hopefully automate it. Thus, I am primarily interested in a bead based RNA extraction kit. I'm looking at Zymo's Direct-zol™-96 MagBead RNA kits. We are currently comparing it to some Qiagen columns, which we consider to be our "gold standard". However, I was wondering if anyone has suggestions or has tried bead based RNA extractions and could provide some insight.

Thanks ahead of time!

Jeremy

[amc463]

Hi Jeremy,

I have the same issue in that we have ~3k samples to extract, and I was wondering what kit/protocol you picked.

[JeremyDay]

Unfortunately, I never found a good solution. I developed a method on our FXP for the Zymo kit. It worked very well for cultured cells, but the second we put clinical samples on, we found that it was co-eluting something with the RNA. This caused a strange migration pattern on Tapestation that resembled degraded RNA. We would then cleanup the RNA using columns and found the RNA to be intact. I still use the kit occasionally for low cell , however, 500k-1M sorted cells in Trizol overwhelmed the system for us. You may have better luck if you have different cell types or if they are cultured. Another potential setup for you may be to use the plate/centrifuge systems or use several vacuum manifolds daisy chained to speed things up (makes me a bit nervous for RNA though).