I have to do transcriptomic analysis of biofilm involving bacteria + filamentous fungi. There are procedures for transcriptomic analysis of biofilm involving bacteria-bacteria or bacteria-yeast (eukaryotic system). Is there any established procedure to purify the bacteria and filamentous fungus involved in biofilm formation. I did not come across any reference regarding this. Can anyone help me in providing purification protocol for the bacterial and fungal partner in the biofilm.
You could isolate total RNA. Then, seperate the fungal RNA based on the polyA tails. Are you doing RNAseq or microarrays? If you are doing RNAseq, maybe just sequence everything, then let the bioinformatics seperate out the two species. If you are doing microarrays, consider using a custom array that has both bacterial and fungal features then probe with the total (mixed) RNA (well, labelled cDNA to be precise). Never done this, just a few thoughts...
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