What to do if you only have a single RNAseq condition?

[bastianwur]

The setup is for sure more complicated, we sequenced more than only a single condition, but it boils down that I need to somehow do something with RNAseq reads for only a single condition.

Background:
The guys in the lab did 3 conditions: Growth of bacterium A in a chemically defined medium (duplo), growth of A and B in the same medium (duplo) and growth of A and C in the same medium (duplo).
B and C cannot be grown in the same medium (or in general on their own), probably due to auxotrophies (but basically nobody knows).

There are some hypothesises here. We expect that B produces a vitamin for A, experimental conditions see a production of a compound which will need this vitamin, and the RNAseq in bacterium A indicates that this works.
Now we also hypothesise that A gives amino acids and some vitamins to B (based on a pathway tools model).
We'll for sure have a look at A, to see if we see some change in expression there in the relevant pathways.

But what do I do with the RNAseq data of organism B and C?
There's only one condition.
They cannot be grown on their own
There's no data whatsoever available from another lab.

I can have a look at the highly expressed genes, but as we all know, this doesn't have to mean very much.

I'd be happy if anyone had an idea what I could do with it.
I don't think I necessarily need to look at it for a nice story, but I'd like to do a full analysis here.

Thanks