I was going to perform Northern Blot. After running the samples on agarose gel, one of the samples did not seem to travel.
Albeit performed northern blot, no signal at all for all the samples.
Using Cy5 labelled probe.
I would say this sample is not clean enough (do you have the possibility to get the 280/260 nm OD?) and the RNA-protein complexes do not enter the gel or that is does not contain RNA and the smear is from DNA (in general degraded RNA make a smear bellow the ribosomal RNAs).
I do agree with the above answer the sample has high genomic DNA contamination. Please check 260/ 280 ratio and redo the RNA prep for the particular sample.
Lane number 5, 6, 7 and 8 seems to have DNA contamination.
For lanes 5, 6 and 8, you do see intact ribosomal RNAs, so for these samples you could do a DNAase treatment to remove the DNA contamination.
Unfortunately, looks like the RNA sample in lane 7 has completely degraded.
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