OHSU

Sample Assessment

The goal of a sample quality assessment is to determine the quantity and quality of RNA/DNA sample material prior to performing the microarray assay.

The concentration of samples submitted to the Affymetrix Microarray Core is measured on a dedicated NanoDrop-1000 or NanoDrop-8000 spectrophotometer that is performance checked using DNA standards prior to collecting sample measurements.  Using concentration data provided by the investigator's laboratory, the most accurate method is determined for quantification of the RNA/DNA sample.  Currently we routinely use both standard absorbance and fluorometric techniques.

The integrity of samples submitted to the Affymetrix Microarray Core is assessed using the Agilent 2100 Bioanalyzer, which uses a chip-based approach to perform fluorescence-based capillary electrophoresis.  A concentration measurement is also generated, which is compared against optical density (OD) measurements obtained from the NanoDrop spectrophotometer.

Tutorial on the general interpretation of RNA bioanalysis trace results

Link to the Agilent webpage that includes a descriptive table of the Agilent RNA bioanalyzer chips

Link to the Agilent webpage that includes a descriptive table of the Agilent DNA bioanalyzer chips

RNA/DNA Sample Quality Assessment Service Cost - $8 per sample, plus a $35 Bioanalyzer chip fee for each group of 10 or fewer samples.

Optional RNA Processing Service: Assistance with determining RNA concentration and clean-up is available through the core lab for an additional fee of $35 per sample.