figure for selection of lysate from 3e6 clones

2013-12-01

azim58 - figure for selection of lysate from 3e6 clones

As of 3-10-13 this will be figure 3a

This figure will make use of data from the 2-29-12 experiment.

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2-29-12 (1st experiment) SMC1fs, 4T1 tumor, naïve sera and secondary
were applied to array. Sera at 1:500 dilution. Secondary at 5 nM.
Conditions: overnight, 23 C, Super G blocking buffer. Obtained some
candidate spots for further screening. (see
http://azim58.wikispaces.com/1st+experiment+2-23-12)

--2 slides Mouse anti-SMC1fs antibody

2 slides tumor mouse
2 slides naive mouse

I'll have to make several graphs and use several programs to get the
final figure that I want.

These graphpad prism files will use the same axis
-axis
--scale of x-axis is from -2.5 to 1.0 with a 0.5 interval

--scale of y-axis is from 0 to 4 with a 1.0 interval
-files
--A graphpad prism file with all of the points can be found here

"C:\kurt\storage\CIM Research Folder\DR\2013\3-9-13\work on paper\figure
for selecting lysate from 3e6 clone\selecting_from_3e6_all_points.pzf"

--3-28-13 I later made another graph with all of the points with the 5

most significant p-value high tumor and 5 most significant p-value high
naive points excluded
"C:\kurt\storage\CIM Research Folder\DR\2013\3-9-13\work on paper\figure
for selecting lysate from 3e6 clone\selecting_from_3e6_all_points2.pzf"

--Another graphpad prism file with the least significant lysates found

here
"C:\kurt\storage\CIM Research Folder\DR\2013\3-9-13\work on paper\figure
for selecting lysate from 3e6
clone\lysates_with_least_significant_p-value.pzf"

--Another file

"C:\kurt\storage\CIM Research Folder\DR\2013\3-9-13\work on paper\figure
for selecting lysate from 3e6
clone\lysates_with_most_significant_p-value_and_high_tumor_intensity.pzf"

--Another file

"C:\kurt\storage\CIM Research Folder\DR\2013\3-9-13\work on paper\figure
for selecting lysate from 3e6
clone\lysates_with_most_significant_p-value_and_high_naive intensity.pzf"

--16E3 lysate

"C:\kurt\storage\CIM Research Folder\DR\2013\3-9-13\work on paper\figure
for selecting lysate from 3e6 clone\16E3 lysate.pzf"

Now I need to combine the images from these different files to make a
composite graph. I'll do this using Gimp.
Composite gimp file
"C:\kurt\storage\CIM Research Folder\DR\2013\3-9-13\work on paper\figure
for selecting lysate from 3e6 clone\selecting lysate from 3e6 clone
composite.xcf"

New composite gimp file without the dots inside the 10 symbols and the
least significant p-value layer removed
"C:\kurt\storage\CIM Research Folder\DR\2013\3-9-13\work on paper\figure
for selecting lysate from 3e6 clone\selecting lysate from 3e6 clone
composite2.xcf"

Inkscape files (oldest to newest)
Inkscape file with labels
"C:\kurt\storage\CIM Research Folder\DR\2013\3-9-13\work on paper\figure
for selecting lysate from 3e6 clone\figure for selecting lysate from 3e6
clone.svg"
New Inkscape file with labels
"C:\kurt\storage\CIM Research Folder\DR\2013\3-9-13\work on paper\figure
for selecting lysate from 3e6 clone\figure for selecting lysate from 3e6
clone 2.svg"
"F:\kurt\storage\CIM Research Folder\DR\2013\3-9-13\work on paper\figure
for selecting lysate from 3e6 clone\figure for selecting lysate from 3e6
clone 3.svg"

log2 fold change image
"C:\kurt\storage\CIM Research Folder\DR\2013\3-9-13\work on paper\figure
for selecting lysate from 3e6 clone\log2 fold change image.png"

log10 p-value image

"C:\kurt\storage\CIM Research Folder\DR\2013\3-9-13\work on paper\figure
for selecting lysate from 3e6 clone\-log10 p-value.png"

Pdf of "Figure 3a"
"C:\kurt\storage\CIM Research Folder\DR\2013\3-9-13\work on paper\figure
for selecting lysate from 3e6 clone\Figure 3a.pdf"

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Screen of Tumor 3e6 library powerpoint slide
"C:\kurt\storage\CIM Research Folder\DR\2013\4-1-13\presentation
prep\Screen of Tumor 3e6 library.pptx"