Hi guys, we recently have discovered Mycoplasma contamination in the cell culture, and an effort is being done to remove it. I was wondering, if I can check the previous ChIP-seq & RNA-Seq samples which might be effected by this. I have want to add Mycoplasma penetrans and Mycoplasma genitalium to the list, if we have lot of reads (not aware of how much should be the threshold) mapping to the genome, it means there is a lot of background from the Mycoplasma, else its fine.
So, do you guys think, I should add some other Mycoplasma species as well, which might commonly effect the cell cultures, as I don't know how similar the Mycoplasma sub-species genome. Also, should I care about the ChIP-Seq contamination with Mycoplasma (may the mycoplasma reads dont map to the mouse genome). The antibody used for the protein pulldown is the anti-GFP.
Are there any other measures or tools to test that, like providing the Genome file as an parameter and the reads mapping to it, should be discarded and the rest should be proceeded with mapping to the genome of organism of interest.