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 ||

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

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.