Mixing DNA & cDNA

[GSviral]

Hi guys,

For my reasearch I am studying both DNA and RNA viruses. Currently I extract both partitions from a sample and treat them as separate samples. For my RNA I perform a whole transcriptome amplification, effectively converting all the RNA into cDNA.

My question is - once I have converted my RNA to cDNA is it possible for me to mix both the cDNA and DNA fractions in order to prepare and run them at once on the GS Juinor platform? A Roche representative advised me not to do this but did not really clarify why. I cannot seem to think of any reason why it wouldn't work or how it would interfere with a successful run.

Has anyone here tried doing this?

Thank you.

[ajthomas]

Are you thinking of combining them before making libraries, or after? I wouldn't combine them before making libraries for a couple of reasons. First, the cDNA will have to be double stranded if it's going to work in the same way as genomic DNA. Second, the amount of data you'll get from each type of sample will depend on how much of each type of DNA is represented in the library, and that will be hard to get right. However, if you're planning to make separate libraries and just combine them for sequencing, I don't see any problem with that. You might get better results if you only combine them after emPCR, and combine the beads in some ratio based on how much data you want from each.