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See a previous study: https://www.ncbi.nlm.nih.gov/pubmed/22923500
Mackenzie explains this analysis of GlyH101 block in a video.
Protocol for Analysis of Experiments using SigmaPlot
1. Open SigmaPlot 13.0 on desktop
2. If adding to an existing notebook, click the second bubble “Open existing” and choose notebook title. If creating a new notebook file, the “New Notebook” bubble should already be chosen.
a. For an example to follow along with, choose the R104C GlyH101 file. The numbers used as examples in this protocol will come from this data file.
3. Click on Data 1* if not already selected. [An excel-type document should be on screen]
4. In the first column, enter the concentrations of the solution being used. These will be the bolded numbers (the second column here is included strictly for reference, it will be explained later). The values are taken from the “mjc111716” tab under Experiment 1 on the left hand side. To find the values for the experiment you are analyzing, go to the table of values page behind the graph of the experiment. From there, look under the column titled, “Soln” and locate the different concentrations used. In this case, it would be “GlyH101 100nM, GlyH101 1uM, GlyH101 5uM, GlyH101 10uM, GlyH101 50uM”
The values here correspond to the values of the GlyH101 concentrations used throughout the experiment. For example, [ -7.0000] refers to the 100nM concentration of GlyH101 (nM is 10^-9, so 100x10^-9 is equivalent to 10^-7). These values were taken from the specified experiment from the purple folder with the title “Experiments by date (Chronological order)”
5. To find the second column of values, look at the same protocol where you found the concentrations. Search for another column titled, “g(m) @ Corr Vrev” [should be 2/3 down]. The values can be located at the bottom of each corresponding concentration value, or the lowest value in the column. This depends on the solution/experiment you are using. Ask Dr. Norimatsu if you are unsure which to use.
If you need reference, try finding the bolded values on the “mjc111716” lab. This will hopefully make more sense when viewing the paper yourself.
6. Once you have the above table present in your excel sheet, you will make a graph of this data. Highlight the entire table and go to the “Create Graph” tab.
7. Choose “Scatter” and then the “Simple Scatter” option.
8. Once chosen, a pop-up window should appear.
9. Make sure “XY Pair” is highlighted and click “Next”.
10. Choose “Y: Column 2: Rows 1-5” Click finish. Note: It will say Rows 1-x, with x being however many values you have for your experiment. It will not necessarily be 5
11. A graph will appear with no connection lines (just data points). Right click one of these data points. Select “Curve Fit”
12. The option “sigmoidal dose-response” should be highlighted. If not, choose this and hit finish.
13. The original graph should appear in a window with a curve fit to it. *Sometimes this fails to happen and you will get the original graph with no lines or a straight line at the bottom. Simply exit out of this graph and repeat steps 11-12 again. If this doesn’t work a second time, seek help. Sometimes the parameters of the graph can mess up.
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