Why this pattern occurs in gel? I mean, why these bands showed this trajectory? And why appeared that bubble, that I circled in red, in the base of gel?
It is something to do with the voltage at which you are running your gels at. What is the voltage you are using? Another reason might be some gel component. Try using fresh buffers.
The voltage that I used was 129 V, and the buffers was fresh also. My lab colleagues suggested that when I prepare the sandwich I have do it more carefully because they think that I closed the sandwich with much pressure and that this pressure can cause these problems.
This could be due to the voltage you are using, if you run the gel with high voltage it can cause smiling of the bands, additionally high voltages can cause excessive heating which can also cause problems and might pay to keep it cool at high voltages. Also make sure you have good contact between the terminals with the buffers. Other possibilities could be the pH of your samples? or you didn't wash the well out before loading the samples. If there are bubbles appearing in your gel then you probably aren't degassing your solutions before casting your gels.
Jason the only bubble in gel that we can see it is that I circled in red in the picture. In regard the voltage, the standard protocol used in the lab is 120V and I used 129V, is it this different in the voltage sufficient to cause that mark and smiling of the bands?
Yes, I think you are right. When I was running the gel I saw that pattern or dye front as you mentioned. But this difference in trajectories between the samples can be explained by high voltage? Or is it due to different time in which each sample entered in running gel?
Voltage is one factor which can cause smiling if it's to high. I'm not sure if the voltage you used it high as the voltage can depend on the SDS-PAGE setup you have and buffers you use. But it doesn't hurt to use a lower voltage. I think it's got more to do with your sample then the voltage. Possibly the pH of your sample is either to basic or to acidic or it could be that something in the sample is slowing it from entering the gel i.e. high amount of DNA or polysaccharide contamination. Is your sample quite thick? You could try diluting your sample or use a larger wells. It looks like the first 8 samples only are running funny. Do they have something in common? Other things are washing wells before loading and making sure there is significant buffer covering all the wells.
No my sample is well diluted actually, I diluted in 20 uL of RNAase free water per sample and add 4 uL standardized sample buffer per sample. The first 8 samples are 4 different groups in duplicate each one. My lab colleagues tell me that the differences between the samples can be because some salt that was stuck in the glass, is it possible?
That would depend on what concentration your sample was before you started. I'm not sure about salt being sick on the glass. But that's right high salt in your samples can also effect. The only other suggestion I have left is maybe to look at trying a different buffering system i.e. Bis-Tris.
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