Validation of most significant spots 6-1-12

2015-01-13

azim58 - Validation of most significant spots 6-1-12

Validation of most significant tumor spots

experiment to validate spots on array. The 5 top p-value increasing from
naïve to tumor, 5 top p-value decreasing from naïve to tumor, and the 5
worst p-value spots were printed onto the array. 5 nM and 1 nM secondary
used. The spots were validated as they should be.

actual experiment on 6-9-12

I will perform an experiment to validate the most significant spots. The
spots to be validated will be chosen from the 2-23-12 experiment (1st
experiment 2-23-12). I will choose the best 5 p value increasing spots,
the best 5 p value decreasing spots, and the 5 worst p value spots. These
will be spotted onto a custom slide many times (maybe 5 or 10) on the top
and bottom and run in the Tecan with dual chambers.

Possible layout
1 slide tumor 5 nM secondary
1 slide naive 5 nM secondary
1 slide tumor 1 nM secondary
1 slide naive 1 nM secondary

In order to print onto the slide, I will need to know the dimensions of
the Grace Biolabs slide.

Image of dimensions found here
"C:\kurt\storage\CIM Research
Folder\DR\2013\1-18-13\data_download\2010_ONCYTE_2060.jpg"

Now I need to select the 5 best increasing, 5 best decreasing, and 5
worsts p value spots.
These spots can be found here:
L:\storage\CIM Research Folder\kwhittem\Records in CIM Folder\Categorical
Records\Biodesign\Immunosignature to Antigen Bridge Project\Tumor cDNA
Library\Application of sera onto array\cell lysate 3-2-12

Top5 Decreasing

Name of Spot
 P Value
 Intensity Difference
 Increase or Decrease in 4T1

1-21-12_RP_2G2
 0.000224
 -762.5
 Decrease

1-26-12_RP_1F1
 0.000447
 -1329.5
 Decrease

1-11-12_RP_3H7
 0.000507
 -1484.5
 Decrease

1-8-12_RP_1B1
 0.000643
 -898
 Decrease

1-11-12_RP_3D8
 0.000695
 -1210
 Decrease

Top 5 Increasing

Name of Spot
 P Value
 Intensity Difference
 Increase or Decrease in 4T1

2-17-12_RP_16C2
 0.000872
 124.5
 Increase

2-17-12_RP_16E3
 0.010051
 46
 Increase

2-17-12_RP_13D3
 0.011491
 39
 Increase

2-17-12_RP_17D6
 0.022714
 168.5
 Increase

2-17-12_RP_3G12
 0.023429
 241
 Increase

5 worst p value spots

Name of Spot
 P value
 Increase or decrease

2-17-12_RP_1A10
 1
 Increase

2-17-12_RP_11H2
 1
 Increase

2-17-12_RP_8A11
 1
 Increase

2-17-12_RP_3B12
 1
 Increase

2-17-12_RP_13D4
 1
 Increase

These spots are located at the following positions in the 384 well plate
(same order as above)
7M4
6L1
8P13
8D2
8H15

4F4
4J6
4G5
5G11
1N23

1A19
3P3
2B22
1D23
4G7

Item
Validation Spot Plate 6-8-12
The spots had the 15 spots above in the following order
1st 5: B1-5
2nd 5: C1-5
3rd 5: D1-5

===========================================================================
Raw data files located here:
S:\Research\Cancer_Eradication\Users\kwhittem\kwhittem\Raw Data Often
Originally on Research Drive\2012\6-11-12 spot validation

Spot validation analysis located here:
C:\kurt\storage\CIM Research Folder\DR\2012\6-11-12
experiment to validate spots on array. The 5 top p-value increasing from
naïve to tumor, 5 top p-value decreasing from naïve to tumor, and the 5
worst p-value spots were printed onto the array. 5 nM and 1 nM secondary
used. The spots were validated as they should be.

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