I am having difficulty with 2D-PAGE. When I start the second dimension, I have noticed two clear lines/ripples that move down the gel above and below where the bromphenol blue marker runs so that there is a clear line, followed by the marker line and then another clear line. In addition, the proteins are not visible. The only thing that stains with Coomassie blue is the line where the marker ran. Does anyone have any suggestions?
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