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