The concentration of CAN step

[NGS group]

Hello, I am trying to construct the library with Nextera XT DNA Kit for Miseq. I got a problem is when I controlled the CAN by Bioanalyzer (DNA Kit 1000, DNA concentration 0.5ng-50ng), no peak was shown. My question is whether there is anything wrong with my library construction, or the DNA concentration of CAN is too low to be detected by Bioanalyzer? Should I continue? which kit are you using for Bioanalyzer?

Thank you very much!

[NGS group]

I used 1ng of bacterial genome for starting.

[kcchan]

The DNA 1000 is probably not sensitive enough to see the peak. We usually have to use the High Sensitivity chip to look at Nextera libraries.

[NGS group]

Thank you for your reply. Should I use nanodrop to measure the purity of library?

[kcchan]

You should be able to measure your library with Nanodrop or Picogreen. However, the broad range of insert size makes it nearly impossible to make any accurate quantification. Illumina has a tech note regarding library validation of Nextera libraries, which may provide some more detailed information.