PCR Screen for SMC1fs 5-3-13

2015-01-13

azim58 - 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"

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