I am working on a pathogenic bacteria , i want to analyze its gene expression by RNA seq, but the main obstacle is that I want to study the gene expression of these bacteria while it is present on the plant., also i want to perform this study in seedling stage of the plant( Eg: Tomato seedlings). I have come across some research articles and i think that dual RNA seq and separation of plant transcriptome from the bacterial transcriptome is possible. But I want suggestion which will be best feasible method to follow. Kindly help me with your advice.
I am afraid you can not obtain enough material (bacteria in plant) for RNA seq. I have a idea, you try to make RNAseq for plant and bacteria and in the step of read alignment, only for bacteria genome.
Dear Pankaj,
we have been working on legumes (Medicago) and its interaction with bacteria (Sinorhizobium) (http://www.plantphysiol.org/content/164/1/400). While RNA-sequencing the plant we could also detect bacterial genes obviously being captured by poly-A selection of mRNA (non-published results). Hence, it seems with our organisms one library preparation with TruSeq could deliver plant and bacteria mRNA profiling at the same time.
All the best,
Claudia
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