Cross-gel Analysis
Idea for comparing more than 3 samples, or multiple replicates
in each experimental group, in which cases not all samples can
fit into one 2-D DIGE gel.
An
internal standard made up of equal amounts of each sample is run
on all gels.
The
internal standard decreases gel-to-gel variation and enables gel-to-gel
matching.
Results
in accurate spot volume visualization and quantitation between
multiple gels.
Experimental Design: An Example
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Cy2
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Cy3
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Cy5
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Gel 1
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Standard
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Sample 1
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Sample 2
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Gel 2
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Standard
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Sample 3
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Sample 4
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Gel 3
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Standard
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Sample 5
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Sample 6
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Standard = S1
+ S2 + S3 + S4 + S5 + S6
Data Analysis
Option 1:
Pair-wise comparison can be done in any of the 2 samples
Option 2: Average protein ratio and
student t-test can be done by grouping samples into groups such
Control and Treatment.
a) Control: samples 1, 3, 5
b) Treatment: samples 2, 4, 6
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Standard (Cy2)
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Sample 1 (Cy3)
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Sample 2 (Cy5)
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Gel_1
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Standard (Cy2)
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Sample 3 (Cy3)
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Sample 4 (Cy5)
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Gel_2
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Standard (Cy2)
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Sample 5 (Cy3)
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Sample 6 (Cy5)
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Gel_3
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