Sample Preparation and Submission
Requirements Before Submitting RNA Samples:
RNA from mammalian cells: Affymetrix recommends using Qiagen’s RNeasy Total RNA isolation kit.
RNA from mammalian tissue: Affymetrix recommends isolating total RNA with a commercial reagent such as TRIzol.
All samples MUST be cleaned up using the Qiagen RNeasy Mini Kit before turning them into this facility. RNA quality should be checked before turning the RNA into us. This includes at least looking at the 260/280 ratio and running the samples out on an agarose gel to check for completely intact RNA. It is highly recommended checking the quality of your sample using the Agilent Bioanalyzer if possible. A minimum of 250 ng of total RNA at a minimum concentration of 83 ng/µl is required for each sample that is turned in. The chips to be used for your experiment are to be turned in with the samples also. The chips are purchased through Affymetrix. You will receive the academic pricing for the chips from Affymetrix. If you are using the Gene 1.0 ST arrays you do not need to purchase the arrays; the arrays are included in the cost of that protocol.
Requirements Before Submitting DNA Samples for Axiom Genotyping Plates
A minimum of 200 ng of DNA at a concentration of 10 ng/µl µl is required for each sample that is turned in. Starting DNA must be double-stranded for the purpose of accurate concentration determination. DNA must be of high purity. DNA should be free of DNA polymerase inhibitors. Examples of inhibitors include high concentrations of heme (from blood) and high concentrations of chelating agents (i.e., EDTA). The gDNA extraction/ purification method should render DNA that is generally salt-free because high concentrations of particular salts can also inhibit enzyme reactions. DNA purity is indicated by OD260/OD280 and OD260/ OD230 ratios. The OD260/OD280 ratio should be between 1.8 and 2.0 and the OD260/OD230 ratio should be greater than 1.5.DNA must not be degraded. The approximate average size of gDNA may be assessed on a 1% agarose gel using an appropriate size standard control. Approximately 90% of the DNA must be greater than 10 Kb in size.