re-amplify low concentrated library

[Jin1]

We are preparing RNA-Seq libraries for Illumina HiSeq 3000. However, a few of the libraries are low in concentration (<5 nM, tested on Agilent Bioanalyzer High Sensitivity DNA chip) and we can not go back for RNA isolation. Can we take aliquot of 2 ul from the library and re-amplify for 5 cycles (and bead purify) to ensure proper yield? And can we use this data for following analysis (compare gene expression levels)?

[luc]

Hi Jin1,

I assume you will be pooling multiple libraries? ; thus, the molarity of the final pool will have to meet the requirements of your sequencing service -- not the individual libraries.
If you also have higher concentrated libraries it is very likely that the final concentration will be no problem.

I would very much avoid amplifying a subset of the libraries in additional PCR reactions and cleanups - this likely could introduce technical variation. I would rather amplify all if absolutely needed.

[Jin1]

Hi Luc,
Thanks for your reply! The re-amplification is only for one or two samples (out of hundred; and are from different biological replicates) which failed to get enough yield.