Titration+of+Secondary+6-1-12

Titration of Secondary 6-1-12

actual experiment on 6-6-12

I will repeat the secondary titration experiment. This time I will compare different concentrations of secondary for their ability to give signal with sera as compared to no sera. I will compare the number of spots two fold greater from secondary alone to secondary with sera. I could also look at p values too.

12 slides will be printed with the whole 3072 library on them. Array Printing Schemes 2-27-12

Here are some figures from Bart and Krupa regarding this topic. Secondary Titration figure from Krupa (she was looking at which concentration would give the most dynamic range) "F:\kurt\storage\CIM Research Folder\DR\2013\4-27-13\wiki_download\krupa secondary titration figure.pdf"

Checkerboard ELISA assay from Bart "F:\kurt\storage\CIM Research Folder\DR\2013\4-27-13\wiki_download\bart checkerboard elisa assay.pdf"

Potential layout of experiment

2 slides with tumor sera and 5 nM secondary 2 slides 5 nM secondary only 2 slides with tumor sera and 2.5 nM secondary 2 slides with 2.5 nM secondary only 2 slides with tumor sera and 1 nM secondary 2 slides with 1 nM secondary

Scanning: When I scan I may want to try a variety of gains and laser powers. Phil also mentioned it could be good to increase laser power and decrease gain. He mentioned that 80l/20g could be interesting. I'll probably try a range of laser powers and gains: 50l/50g since I have done this in the past, 50l/25g since I have done this in the past, 80l/20g, 80l/50g, 80l/100g, 100l/20g, 100l/50g, 100l/100g. I can then see what looks like it gives a good dynamic range and little noise. see choosing laser power and gain

Location of raw scan data: S:\Research\Cancer_Eradication\Users\kwhittem\kwhittem\Raw Data Often Originally on Research Drive\2012\6-8-12 Secondary Titration The array core will align my slides. The location of these slides is here: S:\Administration\PeptideArrayCore\2012 sample run\4T1-cancer-Kurt-04262012\6-8-12 Secondary Titration

Analysis of data C:\kurt\storage\CIM Research Folder\DR\2012\6-9-12\sec titration analysis