Hi,

This shouldn't happen in the ideal scenario. Most of the pipeline will provide the expression only for mature miRNA only. I would suspect, check your differential whether it is Ctrl vs Trtd or otherwise. If this is correct please provide the information about your micro array design info as well as data analysis pipeline. That would help to troubleshoot.

Cheers!!

Vivek

hi

changing technologies and types of analysis can produce this trouble. try to align the probes and primers used in both experiments to get an idea.

fred

Hey Malay,

Which Platform did you use?

in Normal Agilent Platform RNA is labeled via ligation of a Cy3-labeled pCp molecule to the 3' end of the RNA molecule. They also have a probe design that you have both sequence and size selection only for mature microRNAs. These probes are Tm balanced by shortening the probe at the 5' end of the mature microRNA too. So it should not theoretically count the precursor! But if you have used CodeLink platform, it can simultaneously profile mature miRNAs and their corresponding precursors.

Cheers

Ali

Hi Dr Gheinai,

Its the Normal Agilent Platform RNA with Cy3 chemistry.

One problem I could suspect is the degradation of RNA during transport or processing; as we sent RNA after isolating from samples (2 days to reach destination).

Thanks

Hi

in normal time with the agilent scanner you have a bioanalyzer, did you check the rin or simply on gel electrophoresis for RNA degradation?

fred

Hi Dr Lepretre,

Yes. We got RIN values >7.5 in the samples.

Thanks

higher than 7.5 is enough, but you can have good rins with a little part of degradation, that could raise to different results from arrays to RTQ..did you check on agarose gel, to see this point and follow the degration between samples (better to analyze samples with the same QC)?

fred