How to Design a Custom qPCR Plate
Design a custom qPCR plate that fits your experiment
Catalogued PCR arrays cover well-studied pathways, but your research question doesn't always match a predefined gene list. Our online plate designers let you build a quantitative PCR (qPCR) plate around your own targets, choose a layout that fits your samples and order it ready to run. This video walks you through the Custom RT² PCR Array designer. The same steps apply to our other plate designers:
- Custom RT² PCR Arrays: Profile mRNA and lncRNA expression with SYBR Green-based RT² qPCR Primer Assays.
- miRCURY LNA miRNA Custom PCR Panels: Quantify miRNA expression with LNA-enhanced primers for high specificity.
- Microbial PCR Custom Array: Detect and identify microbial species and genes in your samples.
How to design a custom qPCR plate on GeneGlobe - Step-by-step tutorial
From gene list to finished plate in 10 steps
In the video, we design a plate for 7 mouse genes from the retinoic acid pathway. We use a layout with 12 wells per sample, which fits 8 samples on one 96-well plate with room to accommodate controls and reference genes for each sample.
1. Open the designer
Go to "Custom Products" on GeneGlobe. Select "PCR" as the application, choose your analyte (mRNA/lncRNA, miRNA or DNA) and the product, then click "Open Designer". Sign in with your GeneGlobe account, which uses the same login as your My QIAGEN account. If you don't have an account yet, registration takes about 30 seconds and only requires an email address.
2. Name your design and select the species
Enter a design name of at least 3 characters and select your species.
3. Choose your starting point
Start from an empty plate, modify one of our catalog products, or load a target list you saved with GeneGlobe's MyBioList function. Accept the terms and conditions and click Next.
4. Select the plate format
Select your real-time PCR instrument, then the layout. The layout sets how many wells each sample gets and how many samples fit on one plate. A 96-well plate, for example, can hold 96 wells for 1 sample or 8 wells for each of 12 samples. If you are not sure which layout you need, the Plate layout optimizer recommends one based on your number of targets, samples and technical replicates, and it reserves space for controls and reference genes.
5. Upload your targets or start with an empty plate
Upload your targets from a CSV file, from "MyBioList" or by copy and paste. Alternatively, click Continue with empty plate and add them one by one.
6. Add your targets
Open the "Search targets" tab or click a well and then the "+" sign. When you click a target in the results, it is placed at the "+" position, in the same relative position for every sample on the plate. To add a target to a specific well, click that well first to move the "+" sign to that position. Targets already on your plate are marked with a plate icon in the tab, so you won't add the same assay twice.
7. Rearrange or remove targets
Drag targets to move them around the plate. To remove a target, click it and select "Remove" in the panel that opens. The panel also shows information about the target to help you decide. You can review and edit everything on your plate in the "My targets" and "Plate summary" tabs.
8. Add controls and reference genes
In "Search targets", click "Controls" and add the controls for your product. For a Custom RT² PCR Array, these are the Reverse Transcription Control (RTC), the Positive PCR Control (PPC) and the Genomic DNA Control (GDC). Then, click "Housekeeping genes" and add the reference genes you'll use to normalize your data.
9. Finish your design
Click "Continue", then "Finish design". If a control is missing or something else needs attention, the designer flags it so you can evaluate it before finalizing the submissiont.
10. Place your order
Order your design right away or come back to it later in your My GeneGlobe account.