Sequencing mouse and homan mixed sample in one lane (or one barcode) by RNA-Seq?

[chipgal]

Hi,
I am currently doing this mouse cells and human cells co-culture and I am looking at the mutual influence of these 2 types of cells on each other. I want to do RNA-Seq on both the mouse and human cells. However, the co-culture is somehow hard to separate to purity and any purification attempt would lead to changes in gene expression. I am wondering if I could seq the mouse and human samples together in one single lane or using a single barcode. In that way, my sample will be a mixed of human and mouse DNA. I wonder how hard is it to do the actual alignment (correctly to the correct species) and is my experiment plan is feasible at all.

Thanks!

[henry.wood]

I was wondering the same recently. I happened to have a lane of mixed mouse and human samples, so aligned each library against the 'wrong' genome just to see what would happen. About 0.4% of the human reads aligned to the mouse genome and about 0.9% of the mouse reads aligned to the human genome.
These are all random genomic reads, rather than RNA, which might be more conserved, but it gives you an idea.