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RNA Assays
Click a question below to see the answer:
Clearly, the ratio of 28S:18S rRNA is important in determining the amount of deterioration in total RNA preps. How important is this ratio for mRNA preps, where rRNA is a contaminant? Is it still a reliable indicator of degradation?
On different runs, we get different values for the sum of the corrected areas in the ladder sample. What is the sum of the area that should be in the ladder sample in order for the concentration/area values to be valid?
Can I detect Cy3 labeled samples?
I have large amounts of free dye after my Cy5 labeling reactions. How can I get rid of the excess dye?
Why does the 28S band of my total RNA run at just about the 4 kb transcript of the ladder although it is 4.7 kb in length?
How can I ensure that the concentration measurement is correct?
How does RNA quantitation on the bioanalyzer compare to RNA quantitation on UV?
I have many spikes or unexpected bands in my sample. What could be the reason?
Some extraction methods show a distinct band in the lower part of the electropherogram. Isolating the same sample with a different extraction method does not show this band. Which is the difference between the two RNA samples?
I am concerned about the fact that we have to purchase the RNA 6000 ladder to the RNA kit from Ambion. Can we run the RNA assay with another ladder and re-program the bioanalyzer?
I am doing microdissection with the Stratagene Kit. The extraction procedure calls for the use of 10mM Tris that appears to be suppressing the bioanalyzer signal. Can you give me any suggestions on how to rectify this?
What is the buffer composition of the RNA sample buffer?
Can you say something about the quality of the Trizol isolated RNA in reference to microarrays? How much impact does co-isolation of tRNA have on the quantitation of RNA that is used for the labeling?
The kit structure as well as the RNA 6000 Nano kit protocol has changed during the last months. What are the differences between the old and the new kit structure?
Does the staining of cells prior to microdissection negatively influence the analysis with the Pico kit?
The marker alignment did not work properly, what can I do?
Why do I see drifts in migration time from lane to lane?
Why does the Pico Assay need Conditioning solution?
One of the RNA markers appears red instead of green, what does this mean?
Why doesn't the bioanalyzer generate an A260/A280 ratio?
Can I trust the ribosomal RNA ratio for the quality assessment of my RNA sample?
How does the native bioanalyzer gel compare to a denaturing slab gel?
Why should the RNA samples be denatured (4 min. @ 65º C) before analysis?
Is it possible to analyze RNA generated from in-vitro transcripts and calculate their ratio?
What are the differences between 'Cy5 labeled nucleic acids' and other RNA methods?
How do I know if I have genomic DNA in my samples?
During an mRNA run, values for contaminating rRNA are given. Are these numbers meaningful when they are less than 5%?
The error values for the migration of RNA (X-axis) in the gel matrix are given on page 68 of the instruction manual as +/- 15%. What are the error values for the fluorescence (Y-axis) and how do they relate to errors in calculation of RNA concentration?
If one de-selects the exclude ladder option on the Global Peak Find tab, what effect does this have on the data? Does this parameter effect concentration calculations, migration times, or only the peak finding algorithm?
What steps and/or calculations are used to determine the 'corrected RNA area'? What is it corrected for and how is it done?
