Bio-Rad Experion RNA Analysis Kits - Manual (Page 56)

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How Experion Analysis Differs from Gel-Based Methods
Though the Experion RNA analysis kits and other gel-based electrophoresis methods both use a gel
matrix and voltage differences to separate RNA fragments according to their charge:mass ratio, there
are a number of fundamental differences between the two methods that may affect how specific
fragments are separated and how data are interpreted (Table A.1).
Table A.1. Comparison of Experion RNA analysis and agarose gel electrophoresis.
Aspect Agarose Gel Electrophoresis Experion RNA Analysis
Sieving polymer (matrix) Formulation can be changed to affect resolution Fixed formulation
Agarose Polymer (not crosslinked)
RNA stain Multiple available Single, proprietary stain
Intercalates RNA fragments Intercalates RNA fragments
Detection Separate staining step; fragments stained after
separation Integrated separation step; fragments stained
during separation
Separate destaining step Destaining not required
Requires photography or other imaging
equipment for documentation, analysis Laser excites the stain, detection using a
photodiode, both incorporated
Types of separation Native and partially to completely denaturing Partially denaturing
Downstream applications Separated fragments available for excision,
electroelution, blotting applications Fragments not available for further analysis
Reagent and sample usage Moderate: ng to µg sample, ml to L reagents Minimal: pg to µg sample, µl reagents
Waste generation Moderate to extensive (ml to L) Minimal (µl)
Overall analysis time Hours (depends on gel size, staining method,
and methods of documentation and analysis) 30 min/chip (11 or 12 samples per chip)
Data analysis Manual; requires additional equipment and
software Automated (with flexibility of manual adjustments)
Experion Automated Electrophoresis System