RNA contamination in cDNA for microarray experiments - RNA contamination in cDNA for microarray experiments (Oct/17/2006 )

We have prepared cDNA sample for microarray experiment and we have RNA contamination before the labelling with the dyes.
Should we eliminate this RNA?
is it a real problem if we let this RNA for the microarray experiment?

the ratio on the bioanalyser agilent is around 2

thank you for helping us

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You should eliminate this RNA if you are considering In vitro transcription reaction for labeling. But if you are sing amino-allyl in-direct labeling than it wouldn't have such profound effect. But in any case RNase treatment would be best.

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how about adding some rnase.

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You should treat your sample with RNAse A (or H) 20 minutes at 37°C just after the reverse transcription to eliminate RNA contaminant.
Karine.

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