Hey there, I have run a gel of 1% composition of agarose for RNA samples and I have found this irregular line and I am confused that what is this, if you have an idea kindly help me to understand this what is this and where I am making mistake.
The file is attached herewith.
The way that the samples are merging together suggests that the samples are either overloaded or that the comb has torn the gel when it was removed and the samples are mixing underneath the gel Make sure that the gel is completely set before removing the comb and running it and that each sample remains in its well. The separation does not look good so ensure that the molten gel is well mixed before pouring it and that the buffer in the gel is the same as the gel tank running buffer
Maybe RNA samples were not denatured before loading into the gel wells? Make sure You use proper RNA loading dye with formamide and heat samples (65oC) for few minutes before loading. If possible, use also DNA or RNA molecular weight-size markers it may tell if the problem lies somewhere else.
I've also seen a similar phenomenon with DNA if the gel combs leave behind something that degrades the nucleic acid as it runs into the gel. In my case, the comb had had tape on it at one point and something left behind did it: new comb, great bands. Make sure the gel box, tray, and comb are new or vetted for RNA. Maybe change apparatus, run some RNA markers, and examine the stained gel before loading your hard-fought and precious RNAs.
What is your stain? I've also seen weird coloring like that when EtBr has been degraded.
As for the rest, see the suggestions by Paul Rutland and Marek Lubośny. The former gives great answers to just about every question I read and he must have seen everything under the sun :) .
Good luck, your tags are great, and this know that this kind of thing happens. I had Whatmann papers that were just slightly too large cause tie-died looking protein bands after Western transfer. It was far out, man.
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