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View additional product information for GeneChip™ Eukaryotic Poly-A RNA Control Kit - FAQs (900433)
16 product FAQs found
Here are the Poly-A RNA Controls final concentrations (in samples):
- lys 1:100,000
- phe 1:50,000
- thr 1:25,000
- dap 1:7,500
The first dilution of the Poly-A RNA Control can be stored at -20 degrees C for 6 weeks (with up to 4 freeze/thaws).
These four controls are only available as a pre-mixed cocktail with the defined concentrations and relative ratios. This combination of concentrations has been tested to provide qualitative information on both sensitivity and dynamic range of the labeling assay. Providing these controls in a pre-mixed format increases ease-of-use and reduces the number of manual dilution steps.
Information on ordering individual poly-A control clones and preparing poly-A stocks is available in Section 2, Chapter 2, and Section 3, Chapter 2, of the GeneChip Expression Analysis Technical Manual.
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The Control Stock and the Dilution Buffer are packaged in the same Kit to provide convenience to customers. Currently they cannot be purchased as separate products.
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The following tubes were used in-house during product development of this Poly-A RNA Control Kit, and we have not tested any other tubes at this time:
Non-stick RNase-free 0.5 mL microfuge tubes, Ambion, Cat. No. 12350
Non-stick RNase-free 1.5 mL microfuge tubes, Ambion, Cat. No. 12450
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The Dil Buffer has been formulated specifically for diluting the poly-A controls to ensure stability and consistent performance. Do not substitute the Dil Buffer with any other buffer when carrying out the dilutions.
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Since the number of samples processed each time may vary drastically at different customer sites, we have decided to provide the Dil Buffer in one bottle. Upon receipt, users are encouraged to thaw the buffer, and then aliquot it in more convenient volumes for long-term storage based on their own usage rate.
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These controls are only designed to provide a qualitative assessment on efficiency of the labeling assays, and NOT for the purpose of serving as a generic quantitative standard curve.
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This product was designed and tested for eukaryotic arrays. The presence of poly-A tails on the transcripts is not relevant to prokaryotic samples. Since the assays are fundamentally different, this kit may not provide similar array results with prokaryotic assays and has not been tested in-house for this application.
Probe sets for all four controls are available on prokaryotic arrays including the E. coli (antisense) and P. aeruginosa arrays. Adding the Poly-A RNA Controls to these samples will theoretically also serve as a valuable positive control. However, customers who are interested in using the controls for prokaryotic applications will need to optimize the spike-in ratios to obtain the best range for evaluating both assay sensitivity and dynamic range. We do not currently provide support on the Eukaryotic Poly-A RNA Control Kit when used in prokaryotic assays.
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We have not tested the performance of this kit extensively with any other kits/protocols other than the Standard and Small Sample Target Labeling assays currently recommended by us. Therefore, we are not able to provide any sample data or support when this kit is used with any other procedures.
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The Signal intensity representative data (globally scaled) shown in the package insert are typical results for the newest probe design from Affymetrix (3' AFFX-r2-Bs). These probe sets are available on catalog arrays including the GeneChip Human Genome U133, Mouse 430, and Rat 230 arrays.
However, with previous generations of probe sets, the Signal values observed may vary from those shown. Nevertheless, utilization of these controls still serves as a good indicator of the experimental process quality, low-end sensitivity, and assay dynamic range. Some of the arrays that have the older probe sets include the Drosophila Genome Array and Yeast Genome S98 Array.
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First, examine the Present call rate of the 3' probe set of the poly-A RNA control transcripts. Following the recommended dilutions, all four poly-A RNA controls should be routinely called as Present in a Standard Assay. The poly-A RNA control present at the lowest concentration, lys, is expected to be called as Present >70-percent of the time for the Small Sample Target Labeling Assay vII, and the other three controls should be routinely called as Present.
Next, the relative Signal intensities of the four transcripts should also be checked such that they follow the same order of increasing poly-A RNA control concentration as expected. Example data can be found in the kit's package insert.
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At launch, the kit's shelf life is six months from the date of manufacturing. We will continue to perform real-time stability studies and anticipate extending the shelf life as we accumulate more real-time data.
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The recommended storage temperature of the Kit is -20 degrees C. If possible, storing the poly-A controls at -80 degrees C will help ensure the kit's long-term stability.
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Detailed protocols for performing the serial dilutions of the Poly-A Control Stock for the expression assays can be found in the corresponding expression manuals.
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The DNA Labeling Reagent has about 12 months of dating from the date of shipment.
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