I wonder anyone has the experience that DNA contamination can be from the reagents, plastic supplies, experimental equipments, or even the construction materials during single cell Whole-Genome-Amplification.
All reagent and solutions should be RNA/DNA free. You have to be careful with keratin cells from the skin (from the operator, specially important when extracting mammal DNA/RNA) and the best is to do all the process in the laminar flow. But the quality of the starting material is the most important.
I agree. That's why we did in a small room under laminar flow. The room is UV treated every night and the operators are wearing a suit that basically covers the whole body. In this way, we did not get DNA contamination from humans or bacteria. Instead, we got DNA contamination from a type of fish, common carp. That is really strange since common carp is not commonly consumed as food in USA. However, there are some common carps in the pond that is not far away.
Di you ask to people of the Sequencing facility if they are carrying a project with that kind of fish. Contamination in sequencers are not that uncommon if maintenance and good practice are not accomplished. It is specially noticeable when the starting material is not that abundant. If you solve the conundrum, let us know. Thank you and good luck!!
Hi Alexandro, apparently nobody I know works on fish genome. However, one possible source of the adaptors used for deep sequencing and that adaptors (or some version of) contain sequences homologous to fish DNA. That's why we got a lot of reads of fish DNA. But this issue is still under investigation and uncertain yet.
Ockham's razor my fiend. This is the most probable explanation. The best is to wash the wash the adaptors with "DNA away" solution and repeat the procedure with a test sequence. I would check your DNA too regarding quantity and quality, because contaminant sequence become predominant mainly when your DNA sample has a low concentration/quality. Hope you confirm this and solve the problem. Good luck!
Hey Yunfu. I'm late to the party, but stumbled upon this thread while having the same issue. Blasted the adapters and, indeed, hit the same Carp sequences. So, I guess if your libraries are crap, you get carp.
Actually, I had run many projects which showed the so-called Carp DNA contamination to some extent. I am now quite sure most of them are from low-quality samples with a somehow enriched Illumina adaptor sequence contamination, either from a very limited quantity of input DNA or from improperly too short fragment length. However, the carp genome itself maybe also problematic, i.e. with over-presented artificial sequences. So, be aware of this issue, and good luck.
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