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cDNA versus cRNA for a microarray - (Mar/05/2009 )

Hi there,

I have been researching the various options for a microarray experiment I am setting up.

It seems there are two main possibilities - I can either label cDNA or label cRNA for binding to my microarray.

I am wondering about the pros and cons of the two methods. So far I get that:

- Using cDNA is cheaper and faster, because you don't have to perform an in vitro transcription step
- Using cDNA requires more starting material because there is no in vitro transcription.

Is there any other differences between the two methods? Binding efficiency? Labelling efficiency? I can't seem to find any publications that compare the methods.

cheers :)


dna-rna hybridization is more stable (stronger) than dna-dna.

rna is more vulnerable to decomposition (rnases everywhere) until bound.

we use crna for gene expression arrays.