Complex samples such as E.coli dry powder - plant tissues - etc. tend to agglutinate during the stacking process due to the SDS-fat mycelles.
After this false starting process the sample form a “channel” in the track.
1. Use a extraction buffer without SDS.
This inhibits the solubilization of fat. Afterwards the fat-SDS-mycelles will disturb the electrophoresis.
The SDS-samples should be produced out of this concentrate.
2. Add 0.6 M Urea to the samples after the heating process.