Experience using RNA-Seq kits with Total Nucleic Acid

[herter]

We are looking to streamline our protocol to make it kit based. Our current home brew protocol works well with RNA and DNA input to look at DNA and RNA viruses. Are there any RNA-Seq kits available that will work well with RNA and DNA input? The company reps aren't very helpful and want us to make two separate libraries, one RNA(cDNA) and one DNA.
Thanks!!

[nucacidhunter]

If your target nucleic acid includes both ds- and ssDNA there are some commercial kits. You might be able to add an RT reaction in front of those kits for preparing library from total nucleic acid preps.

[herter]

Thank you for your suggestion! That is what we are currently doing in the lab. We are hoping to find an RNA-Seq kit that would also accommodate the DNA as well. Just to streamline the process and make everything based from one kit. This may not be possible, though.

[nucacidhunter]

All current RNA-Seq kits have been designed for expression/transcript analysis. I think for your application there is not enough demand to encourage commercial producers but technically it is possible.