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Old 06-27-2012, 02:42 AM   #1
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Location: MA

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

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.

chipgal is offline   Reply With Quote
Old 06-27-2012, 08:20 AM   #2
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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.
henry.wood is offline   Reply With Quote

2 species, rna-seq

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