Tumor vs normal on 2-17-12_16E3 spot 2

2015-01-13

azim58 - Tumor vs normal on 2-17-12_16E3 spot 2

Experiment actually performed 7-27-12

This time when the 2-17-12_16E3 library is printed again some negative
controls will be included onto the slide as well. I made a negative
control plate.

Item: E coli lysate negative control plate 7-25-12 KW

1:500 sera
5 nM secondary
Naive slides in slots 1-4
Tumor slides in slots 5-8

Here is the gal file for 3K lysate with e coli negative control 7-30-12

Slides were scanned with 100% laser power and 50% gain.
The 1st scan of the slides can be found here:
S:\Research\Cancer_Eradication\Users\kwhittem\kwhittem\Raw Data Often
Originally on Research Drive\2012\7-28-12 tumor lysate scan
The alignments were performed by Mara and are found here:
S:\Research\Cancer_Eradication\Discovering tumor specific antigens\Tumor
cDNA Library\Application of sera onto array\7-28-12 tmr-nv-lst

After this 1st scan, I saw that the slides looked much better than last
time. There weren't so many streaks and spots of uneven intensity.
However, I noticed that the naive slides increased in intensity in order
from 1-4. An image of this can be found here
"L:\storage\CIM Research Folder\DR\2012\7-30-12\lysate slides\comparison
of 1st 4 naive slides.png"
Perhaps I started scanning the slides when they were still a little wet,
and the detected intensity increased as they dried. The tumor slides
which were scanned later do not display as much of a difference.
"L:\storage\CIM Research Folder\DR\2012\7-30-12\lysate slides\comparison
of 1st 4 tumor slides.png"
I will try to rescan these slides and compare.
After the 2nd scan, the 1st two naive slides still look fainter than the
other two so I guess this was not due to a drying issue. The slides also
had much higher intensity in general though.
"L:\storage\CIM Research Folder\DR\2012\7-30-12\lysate slides\comparison
of 1st 4 naive slides after 2nd scan.png"

Analysis
"C:\kurt\storage\CIM Research Folder\DR\2012\8-2-12\tumor naive lysate
analysis 8-2-12.docx"
and
"C:\kurt\storage\CIM Research Folder\DR\2012\8-2-12\tumor naive lysate
analysis 8-2-12.xlsx"
Here are some additional notes on the analysis.
"C:\kurt\storage\CIM Research Folder\DR\2012\8-2-12\additional notes on
analysis 8-2-12.txt"

Here is a histogram of the intensities. The tumor sera did have more
overall intensity in this experiment.
"L:\storage\CIM Research Folder\DR\2012\8-2-12\intensity histogram
7-28-12.png"

9 spots from this experiment were chosen for further analysis.
3 best p value spots
21E11
22H10
21G4
3 best fold change increasing from naive to tumor
11G12
7F12
7E12
3 spots with highest average intensity in tumor
10A5
13A5
29A5

I noticed that the 3 spots with highest average intensity in tumor are
all A5 spots. I will look at these spots on the array to see if I notice
anything unusual.
I couldn't detect anything unusual so I think the fact that these are all
A5 spots is really just a coincidence.
L:\storage\CIM Research Folder\DR\2012\8-9-12\check of A5 spots

All spots
21E11
22H10
21G4
11G12
7F12
7E12
10A5
13A5
29A5

Item: Selected 16E3 Spots Glycerol Stock 8-9-12

===========================================================================
8-11-12
Item: Individual colonies from selected 16E3 Spots Glycerol Stock 8-11-12

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