Nanodrop vs BioAnalyzer
I ran an InVitro Transcription (IVT) reaction to make RNA for a protocol I'm using. After IVT I used Ampure beads to purify the reaction. I then quantified my RNA using the Nanodrop and it showed a concentration of 100ng/ul. When I ran the sample on a NanoChip on the bioanalyzer, I got a blank trace. I assume this means I only have free nucleotides in my sample but I'm a little perplexed because I thought that after a bead clean up I would have removed all free nucleotides. Any ideas why I don't see RNA on my NanoChip and why I didn't clear free nucleotides?