Titration of Secondary 6-1-12

2015-01-13

azim58 - 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

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