Our lab performs microbiome analysis on a variety of samples; therefore, we do a high number of DNA extractions which require very low levels of background contamination. We are thinking about purchasing an automated system for DNA/RNA extractions and I was hoping to get the opinions of anybody who has experience using various systems. We have tested the Promega Maxwell, which was affordable and user friendly, but we are concerned about the background contamination affecting our sequencing results. While we haven't tested a Qbot, I suspect that it may have similar contamination issues merely due to the design of the system. We have also considered robots, such as those made by Corbett, that can perform other pipetting functions in addition to DNA extractions, but our budget isn't quite large enough for such a nice system. We are also considering the typical high-throughput methods using 96-well plate spin columns, but we'd like to see what is available in the way of automation as well.
Can anybody share their experiences with the Maxwell, Qbot, EPmotion, or other automated systems? Please tell me the good and the bad.
Where does the contamination occur in the Promega Maxwell? Thanks, Meredith Hullar
There could be multiple sources of contamination with the Maxwell. I think the main cause, which Promega is working on now that we shared our data with them, is that they weren't producing their reagents in ultra clean rooms like some other companies do. The reagents weren't designed for high-sensitivity detection of microbes in mind. They are currently working on fixing this issue and we plan to re-demo the instrument at a later time.
Another source of contamination results from the fact that the reagent cartridges must be opened outside the instrument before loading them into the machine. The machine itself has a HEPA filter and UV light, but unless you can fit it inside a PCR hood (which is difficult due to the footprint of the machine), you have to expose your reagents to an unfiltered environment. This isn't an issue for most samples, but since we sometimes look microbes in bioaerosols, it's very problematic for us.
Another source could be from within the instrument itself. As the the robotic arm moves magnetic beads over various solutions, it's possible that cross contamination is occurring. I think this is more likely with our fecal samples that contain high biomass as Promega has worked hard to avoid those issues.
Do you use a Maxwell, Meredith?
Have You tested the Qiagen BioRobot M48 workstation. It is working with the magnetic beads. It allows automated nucleic acid purification and is very hekpful in DNA extraction from cell culture . We were thinking about purchasing the system, but while we are working with human cancer tissues the most important part of nucleic acid isolation is the homogenisation step. Though usually we're extracting no more that 4 tissue at a time, and we're using the spin-column kits - so using the robot station wouldn't be efficient.
Maybe You can find more helpful info in this paper: http://www.forensicscience.pl/pfs/76_parys.pdf - in this paper authors compared phenol-chlorofom method to the magnetic method and they were using the mentioned above Qiagen robot.
You can also tested the QIAcube of QIAEGN, very useful by the numbre of sample is 12 at the same time
I'm working on DNA extraction from plant material using the Maxwell and we never had a contamination problem. I suspect that the contamination happens before or after automated DNA extraction. For us, the Maxwell works pretty well.
Karolina, we have looked at the Qiagen Biorobot but haven't tested it. I was hoping to find somebody who has! We have a similar problem with some of our tissue samples with respect to adding a homogenization step prior to loading the sample into the DNA extraction device. We are currently using spin columns for some samples and phenol/chloroform for others but we anticipate doing hundreds or thousands of extractions in the future and are looking for an automated solution.
Patrick, most of the contamination was a result of the proteinase K step at the beginning of the protocol, which Promega is working on fixing. Some of our samples require the buccal swab kit from promega, which has this basket spin step to remove any swab material and has also been shown to result in contamination.
I mostly use both of Kingfishers, and we have them in "clean rooms", designated for sensitive applications only (RNA extraction or smth). So that solves the contamination problem. And I really like the Duo one - cause it's so small, and only one plate is needed.
Colleagues of mine have them in their labs and use them for DNA extraction. Haven't complained about contamination either.
Hope that helps.
Hi Cassandra the Kingfisher Flex and Duo work really well, with MagMax and other magnetic bead based kits
Has anyone used IndiMag 48 for RNA purification? How open is it for MagMax RNA kits? Is it comparable to King Fisher DuoPrime?
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