You can find the DIGE Tutorial files in the folder Tutorials in the software installation directory. They come from an experiment that aimed to study protein expression changes between control and treated groups of bacterial cultures.

In this study, eight sample lysates were prepared; four were derived from treated bacterial cultures and four were derived from un-treated (control) bacterial cultures. Aliquots from each sample were taken and pooled to prepare a standard sample (pooled internal standard). The samples were run on four gels. The control and treated samples were alternatively labeled with Cy3 or Cy5 (dye swap) to avoid dye-bias. The standard was labeled with Cy2 and run on each gel in the experiment. A preparative gel (Pick), including reference markers, was run on the pooled sample and post-stained with a Fluor total stain to pick spots and identify them by mass spectrometry (MS).

Gel Cy2 Cy3 Cy5
Gel 01 Pooled internal standard Control A Treated A
Gel 02 Pooled internal standard Treated B Control B
Gel 03 Pooled internal standard Control C Treated C
Gel 04 Pooled internal standard Treated D Control D