double 18S peak on Bioanalyzer

[crimor]

Hi everyone,
total RNA (Qiagen RNAeasy kit) from a human cell line:
I have a strange double peak for 18S rRNA on BioAnalyzer.
What could the lower MW peak be?
Its abundance varies a bit from prep to prep,
but seems to be consistently present in this cell line, even with TRIZOL extraction.
Any suggestion will be welcome !
Thanks a lot,
Cri

[neurodoc44]

RE: double 18s peak on bioanalyzer

Hi Crimor,

We see a very similar double 18s peak in our TRIzol/RNAeasy extracted samples from a rat hippocampal neuron cell line.

The interesting thing is we see the double peak in RNA from differentiated neuron cultures, but not from RNA extracted from cells that have not gone through the differentiation conditions.

Unfortunately I have no answer for you either. I know this kind of profile can sometimes be expected for some insect RNAs, but not typically for human or rat RNA. Our other guess was trying to extend the denaturation of samples prior to loading on the chip to reduce secondary structure that can also lead to profiles like this, but that did not help either.

So hopefully someone else can answer this one for us!

[pmiguel]

The hypotheses I would consider:

(1) Extra 18S cleavage event in some cell types/conditions.

(2) Unrelated, highly expressed RNA that just happens to co-migrate with the 18S.

(3) (This one would be my guess.) rRNA cluster, normally silent, that is expressed only in these tissues/conditions -- slightly different length.

(4) Slave transposable element excision that occurs only when the master element transposase is expressed.

Well, I am getting a little too exotic now. I will leave with those 4.

--
Phillip

[mcgarryg1]

I have a common trend in my RNA bioanlyser results showing a double peak at 18S in all samples.

Has anyone found a reason behind this?