PCR+Screen+for+SMC1fs+5-3-13

5-3-13

This was a screen of the 96 wells from the 2-17-12_15 plate for the presence of SMC1fs.

Minipreps from all of the wells in this plate found here 2-17-12 ("2-21-12") Plate minipreps at 4-30-13 Box 1 at -20 C KW 4-30-13 Box 2 at -20 C KW

Spreadsheet of wells containing SMC1fs. "F:\kurt\storage\CIM Research Folder\DR\2013\5-5-13\smc1fs screen\smc1fs screen results 5-5-13.xlsx"

Now I would like to correlate this information with the actual antibody array screening results.

I may need to refer to the original gal file of the 3K lysate library 3K Lysate gal file with qcorrect esq 5-5-13 Actually, I will probably want to refer to the gpr files from the experiment in which I put the SMC1fs #|antibody onto the array. Need to find which I experiment I want to use the data from. #|referred to Short communication paper associated with DNA Vaccine Conference 2-14-13 From my #|rough #|draft on this page I found that the experiment I wanted to use was the 2-29-12 experiment. 1st experiment 2-23-12 From there I can see that the data I will want to use is stored here F:\kurt\storage\CIM Research Folder\DR\2012\8-25-12\8-25-12_1402\Application of sera onto array\cell lysate 3-2-12

Analysis of sera #|samples "F:\kurt\storage\CIM Research Folder\DR\2012\8-25-12\8-25-12_1402\Application of sera onto array\cell lysate 3-2-12\SMC1fs c 4T1 c and Naive Analysis 5-5-13.xlsx"

5-6-13 Wrote a little bit of code to #|check for the presence of SMC1fs in all #|the pools. "F:\kurt\storage\CIM Research Folder\DR\2013\5-6-13\screening pools\checking presence of SMC1fs code.txt"

More code to check more SMC1fs state #|possibilities "F:\kurt\storage\CIM Research Folder\DR\2013\5-6-13\screening pools\checking presence of SMC1fs code 2.txt"

regular expression to #|replace all lines that don't have a "1" at the end f ^.+[^1]$\r\n r

I also performed some SMC1fs screens on 3-30-12 SMC1fs PCR in 4T1 cDNA lysate pools 3-30-12

I wanted to make a graph with only the SMC1fs unknown points (most of the points), and then add the other points on top of that. "F:\kurt\storage\CIM Research Folder\DR\2012\8-25-12\8-25-12_1402\Application of sera onto array\cell lysate 3-2-12\SMC1fs c 4T1 c and Naive Analysis only SMC1fs unknown 5-5-13.xlsx"

Here's an Inkscape file where I am organizing some of the graphs. "F:\kurt\storage\CIM Research Folder\DR\2013\5-6-13\screening pools\smc1fs screen graphs 5-6-13.svg"

I can see that for the naive to SMC1fs comparison that some of the spots containing SMC1fs (validated by PCR) have more significant p-values and fold change values than the other spots. However, there are also many spots which contain SMC1fs which do not have a more significant p-value or fold change value.

I made a short little data update powerpoint "F:\kurt\storage\CIM Research Folder\DR\2013\5-7-13\Data Update 5-7-13.pptx"

Data update without source info "F:\kurt\storage\CIM Research Folder\DR\2013\5-7-13\Data update without source data 5-7-13\Data Update 5-7-13.pptx"