As explained in an animation on the Invitrogen website, qPCR starts with the same PCR ingredients we already use, but incorporates a fluorescent dye called SYBR green that intercalates between the DNA bases as new strands of DNA are built during PCR cycling. In a special PCR machine, a camera captures the fluorescent signals during the PCR cycles and translated into a graph like this: 
The software calculates a threshold line, the point at which the reaction reaches a fluorescent intensity above background noise. The PCR cycle at which the sample reaches threshold is called the Cycle threshold or Ct, as follows:
The Ct value will be used in the quantitation calculations, and can also be used for simple presence/absence detection for the sample.
Because SYBR green is not target specific, we will run a melting curve analysis (shown below) to ensure that the target locus was amplified. The peak on the graph indicates the melting point of the amplified locus, which is the same for all the graphed samples in this example. If the PCR contained contaminating DNA or primer dimers, these would show up as additional peaks, separate from the amplicon of interest.
- Watch Analyzing quantitative PCR data
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- We will use the relative change in gene expression using the delta-delta Ct method described second in the video.
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- OPTIONAL: If you are curious and want more info before lab, you can review the reading quantitative PCR Tutorial, highlighted sections on pages 3-6 and 11, for additional background on qPCR data analysis.