I want to use a gene array to determine differential gene expression of leukocytes in sepsis, but the bioanalyzer results all show significant bacterial RNA contamination.
My model induces sepsis by puncturing the mouse cecum to leak feces into the peritoneal cavity. I collect my cells from the peritoneal cavity.
Any ideas on how to remove the bacteria prior to RNA extraction?
It depends on what kind of leucocyte you are interested in.You could isolate specific populations of leukocytes with magnetic beads and washing exaustively I think you would get rid of bacteria. However if the leukocytes you are working on are phagocites, the bacteria RNA you are seeing probably is inside the phagocite. I don't know if isolating mRNA could help...
Thanks Rosa. I'll look into the bead-based separation, although I've noticed those kits are rather pricey and this is just a small pilot experiment. I'm not too concerned about the bacteria already inside the cells as their numbers are small compared to what is outside
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