Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Protocols

Tuesday, April 23, 2024 Home Members Project Protocols Progress Discussion References

Protocols Things that need to be written Quantitating DNA How to run a gel How to do AFM (when we learn this) How to analyze fluorescence experiments (when we learn this) How to perform gel purification How we ran experiments... = SPEX protocol 1. Turn on the lamp (back side). Wait for 30 min Bottom big on/off button is for the machine. It is always on. Top small one is for the lamp. If there’s somebody who will use the SPEX tomorrow, then do not turn off the lamp after the experiment. 2. Turn on the computer if it’s not on. 3. Software: Instrument control center Default: Click OK 4. Temperature set up Click the third square icon called “Visual setup” Click the middle square Temperature control icon: Turn on and Set to 25 degreeC Choose T bath (internal). NOT Probe (external). 5. Wash the cuvettes. Be careful! Hold only top or bottom. DW (10 times) 70% ethanol (twice) DW (5 times) 70% ethanol (once) While you wash, you can touch the side. Hold it in a stable way. Let it dry (upside down) 6. Dry the cuvettes using lens paper. 7. Click second square icon called “real time display”. High voltage: HV on, S 950, T 950 Bandpass : Set 2 for everything 8. Click the last square icon called “run CWA”. Open a file called “ROX_CWA” from e:\SPEX DATA\biomod Optional mode: kinetics, Integration time: 10s Define: Repeat acquisition: 1 min (minimum) for total of 180 min (3 hours) 9. Mixing: Hold top. 350ul of 1000ul pipette all the way in. Mix it for 30 times. 10. Put the cuvettes. Logo faces out! 11. Start acquisition. Run sample. Range of the real data should not exceed 1 million (1000,000) Number we see is S/R  will be (100 million) 12. Add more samples in the middle of SPEX experiment When the status is “waiting”, click “stop”. Don’t click anything else. Add and mix. After you put the cuvettes inside the box, click “no”. 13. Save the data When the status is “waiting”, click “stop”. Click “yes” Save data in two forms (DWA datafile, multi~ test) Check if the data is properly saved: Check the last data. If you want to see the reference, go to options: view option and display raw R. How to Open SPEX Data in MATLAB Open up MATLAB and use File->Import Data Navigate to the raw-text (.txt) data file and open it The table on the right should show eight rows, where the odd ones are the times associated with the signal from the row under them. The top set is sample 1; the next is 2, the next is 3, the bottom set is sample 4. Press "next." Optionally right click on "data" and rename it to whatever you want. This isn't necessary unless you're afraid of your data getting overwritten eventually when you import another set. Click "finish." Your data should be visible in the "workspace" window with the name "data" or whatever you might have renamed it to. Right click on it -> "open selection" to view it. To plot a single sample's data, use this, where "data" is the name of your data variable: <syntaxhighlight lang="matlab">plot(data(1, :), data(2, :))</syntaxhighlight> To plot all four samples' data on the same plot, use this: <syntaxhighlight lang="matlab">plot(data(1, :), data(2, :), data(3, :), data(4, :), data(5, :), data(6, :), data(7, :), data(8, :))</syntaxhighlight>