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minimum information for publication of Microarray - (May/24/2012 )

Is there any minimum information for publication of Microarray like this one below for qPCR???

The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments.

http://www.ncbi.nlm.nih.gov/pubmed/19246619

My supervisor asked me to do some QPCR to show a over expression of a gene that he has seen during Micoarray that one of his PhD student has done.

I have repeated it but there is no over expression. But in Microarray there is a 40 folds over expression between treated and non treated cells.

But my supervisor insists that I should repeat qpcr until the result is like microarray.

The PhD student is in third year of PhD and I am in the first year, so they think that my results are not trustable.

I have read in some papers that before publishing microarray data, we should verify data by RNase Protection Assay and QPCR.

What is your idea?

I have told them that maybe the cells were contaminated with Mycoplasma. Mycoplasma is a real problem:

http://babakmemari.wordpress.com/2012/05/22/unexpected-presence-of-mycoplasma-probes-on-human-microarrays/

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Babak

-memari-

Your problem is a common one. I think rather than trying to prove that microarray data can be inaccurate, you should focus on demonstrating that your qPCR abilities are trustworthy. There are clearly 2 possibilites here: either the microarray data generated by the "senior" PhD student are trustworthy or the qPCR generated by the "junior" PhD student are accurate. It is true that microarray data need to be validated by qPCR, since there will always be a certain amount of "noise" and biological variability that will give false positives. Unfortunately (for you), first year PhD students are also associated with a considerable amount of "noise". My advice to you is to become an expert of qPCR. If there are positive and negative controls in your experiment, make sure you can demonstrate they are "moving" in the right direction by qPCR. If you gene of interest is not giving the "right" response demonstrate this with more than one primer pair and talk to experts to make certain that your assay is being performed correctly. The truth is that you can spend a year becoming the most trustworthy qPCR scientist in your lab and demonstrate that the microarray data were inaccurate, but then you would have no publishable data. It sounds like your boss just wants you to "get the right answer", so he can put your name on a paper.

-doxorubicin-