Can I combine 16S and 18S rRNA in one sequencing run?

[cement_head]

Hello,

I wanted to examine a complex system for the presence of both prokaryotic and eukaryotic microbes.

Is it possible to isolate enviromental DNA and then do both the 16S rRNA (http://www.earthmicrobiome.org/emp-s...protocols/16s/) and the 18S rRNA (http://www.earthmicrobiome.org/emp-s...protocols/18s/) library construction in a multiplexed manner and then combine them for sequencing on a MiSeq?

Are there any barriers, or reasons why not to doing this?

Thanks,
CH

[cement_head]

*bump* *bump* *bump*

[cliffbeall]

There shouldn't be any problem. We just did a run with two different bacterial amplicons on the MiSeq and it was fine. If you're doing the Illumina 2 PCR system you can use the same index primer set for both.