Based on the procedures for 2D gel electrophoresis described in [14 (link)], we optimized conditions and settings specifically for the zebrafish samples. After the last washing step of the deyolking procedure, care was taken to remove the supernatant completely in order to keep the salt concentration as low as possible. Total protein precipitation, to reduce salts and other interfering substances, is not required for analytical gels but may be applied for preparative gels. We recommend as starting material 50–100 embryos for analytical gels and 500 embryos for preparative gels.
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