QIAcube from Qiagen

January 31, 2013

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University of Virginia
Infectious Diseases
Laboratory and Research Specialist
qPCR amplification of Bacteroides DNA extracted from mouse stools using the QIAGEN QIAcube (qPCR performed on Bio-Rad CFX 1000)

Company:

Qiagen

Product Name:

QIAcube

Catalog Number:

9001292

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Much of our research involves quantitative microbe detection from stools shed by mice – either pathogen or intestinal flora. Our lab routinely has a large number of samples (approx. 50-100 per day) which need to have total DNA extracted for further qPCR quantification. This is a tedious and time consuming process when done manually. The QIAcube is an automated system which can extract DNA or RNA from up to 12 samples simultaneously, reducing the amount of time a researcher needs to spend loading samples and washing columns.

Experimental Design and Results Summary

Application

DNA extraction from stool samples for quantification by qPCR

Starting Material

Our stool samples first need to be prepped before they can be loaded into the QIAcube. This involves homogenizing the stool in 400 µL Qiagen’s Stool Lysis Buffer (ASL), which we incubate on a heated laboratory shaker at 83°C for 5 minutes. We then centrifuge the homogenized stool at 14,000 RPM for 2 minutes and transfer the supernatant to a 2 mL microcentrifuge tube, which is then loaded into the QIAcube.

Protocol Overview

The QIAcube is normally prepped by loading the different wash steps and diluents, custom pipette tips, and rotor adapters which are loaded with a wash column and 1.5 ml microcentrifuge tube. You can then select your desired program (in our case, DNA Stool Extraction) from an LCD touchscreen window on the machine. The entire prep process, from homogenization and incubation to hitting start takes about 20 minutes. Extraction from this point takes about 90 minutes.

Tips

It is best to wait for the machine to finish confirming it has all of the parts and reagents it needs to begin a run before you leave to do something else: if something is not going to work during the run, most likely it will be because of a missing reagent or pipette tip. It’s also important to load the samples into the machine using 2 µL microcentrifuge tubes rather than 1.5 µL tubes – the machine will not be able to complete a run since the pipette tips the machine uses will be jammed into the bottom of the 1.5 µL tubes and the run will stop. It is important to make sure your sample is completely homogenized before loading and that there isn’t any debris – a piece of collagen from a tissue extraction can clog the pipette tip or the filter.

Results Summary

Measuring nucleic acid purity with a spectrophotometer, we usually find OD readings at or above 1.94 (this is about 70% purity), or about the same as many other DNA mini-prep kits commercially available.

Features Summary

This instrument allows for high-throughput extraction of DNA and RNA. If you are performing extractions on a daily basis in your lab, some sort of automation is very convenient. The instrument comes pre-loaded with standard protocols for DNA and RNA extraction, but you are able to customize protocols based on your extraction method (for our lab – DNA extraction from stool). Our lab has two of these machines since they are used so often. There are some drawbacks. Only 12 samples can be run at one time per machine. Rotor adapters and pre-loaded pipette tips must be purchased from Qiagen. The instrument will stop if loading has not been done correctly or if there is a problem with the run – the instrument will beep only once if a run is stopped. Recently we have had some issues with the transfer of spin columns from the cassette to the elution tube; we have contacted a Qiagen representative to see if this can be corrected.

Additional Notes

None

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qPCR amplification of Bacteroides DNA extracted from mouse stools using the QIAGEN QIAcube (qPCR performed on Bio-Rad CFX 1000)

Summary

The Good

Compact, does not require an external PC to use, automation of a tedious process.

The Bad

Can only run 12 samples at a time; must purchase disposable rotor adaptors and pipette tips from Qiagen, machine must be watched as a run starts to make sure there are no problems.

The Bottom Line

This device is worth serious consideration if you perform extractions on a regular basis.

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