Running a RNA Nano chip is very similar to running a DNA chip on the Bioanalyzer. However there are some things to keep in mind:
1. Clean everything with RNAse Away! before you start. I clean the chip loading stand as well as everything I am working with.
2. Make sure the reagents are at room temperature before you start to make the gel.
3. Before loading the chip, pipette 1.2 uL of each sample as well as the ladder into PCR tubes and incubate in the thermocycler for 2 minutes.
On the last point, I aliquot my samples into the PCR tubes and incubate them right before I load the gel. The instructions say to denature all the ladder in one go, but I have had better results when I denature an aliquot with my samples right before I run the chip.
Attached is a chip of 12 conifer leaf tissue extractions that worked out pretty well.