PDQeX Nucleic Acid Extractor

Product Manual

prepGEM
forensicGEM
phytoGEM

Contents
Introduction to the PDQeX
Page 3
Process Overview
Page 4
Device Set-up
Page 5
Loading and Unloading
Pages 6-8Settings
Page 9Date and Time
Page 10UV Treatment
Pages 10-11
Pre-defined Programs
Page 12
Custom Programs
Page 13
Error Messages
Page 14
Cleaning, Sterilization, and Maintenance
Page 15
Contact
Page 1602

Contents

PDQeX Nucleic Acid Extractor
The simplicity and minimal sample manipulation requirement of the PDQeX make it anattractive option for obtaining DNA samples.
Jo-Ann Stanton, PhD
Department of Anatomy, University of Otago
New Zealand

MicroGEM's PDQeX Nucleic Acid Extractor brings together
powerful enzymes with an innovative extractor cartridge andpurification matrix. The temperature-driven single-tube systemproduces extracts in significantly less time (minutes, not hours)
than other extraction methods.

PDQeX Extraction Reagents consist of a cocktail ofthermophilic proteinase and mesophilic cell wall degrading
enzymes that systematically lyse cells, destroy nucleases,
digest proteins, and release nucleic acids. Each reagent kitis specially formulated for specific sample types.
PDQeX Extractor Cartridges, made from thermoresponsive polymers, pump extracted DNA through thepurification matrix while removing cell debris andinhibitors.

Specifications
Sample capacity
For use withInterface
Voltage (24 V DC adapter included)
Power
Thermal profiles
Programmable thermal range
Dimensions
Weight24 samples, standard 96 well spacing
24 PDQeX cartridges (200 μL)
5" touch screen (color)
100-240 VAC, 2A, 50/60 Hz
96 watts at peak draw
Pre-installed and user programmable34-120° C
22 x 18 x 18.5 cm (L x W x H) (8.5" x 7" x 7.25")
4.8 kg (10.6 lbs)

Perfect for a wide range of sample types including:Plant material

Animal tissue

Introduction to the PDQeX

Forensic evidence and human ID

Bacteria

Viruses

Insects

03

Process Overview
Step 1: Sample preparation
Sample preparation prior to extraction varies from sample to sample. Refer to each kit 's Quick Start Guide for
specific sample preparation guidelines.

Step 2: Cell lysis, DNA extraction and purification
This multi-stage process takes place inside the extractor cartridge.
1. The cells are lysed by a cocktail of enzymes. This cocktail varies for different substrates. For example, thelysis of leaf tissue requires a complex mixture of hydrolases and a specific program on the PDQeX to activatethem.
2. A temperature regimen is carried out by the PDQeX for different enzymes at different temperatures. The final
temperature inactivates the enzyme leaving a lysate containing DNA, cell debris, and denatured protein.
3. On completion of the extraction, the extractor cartridge forces the extract through a special column. Thecolumns are tailored to each sample type and designed to remove anything that may inhibit Taq DNA
polymerase or enzymes used in most other downstream processes.
4. The samples are ejected into PCR tubes in a standard format (8 strips or 3x8 strips).

Step 3: Quantification
The DNA is now ready for quantification. Because the heat step denatures the DNA, do not use OD or fluorescentdye methods. The best method for quantification is qPCR. With normalized samples, quantification is notalways required and the DNA can be used directly.

04 Process Overview

Operating Instructions
Device set-up
Connect the PDQeX to the power supply and switch on. Only use the power supply provided with the PDQeX.
WARNING: The PDQeX should be installed with easy access to disconnect from thepower supply.
Back of the PDQeX

USB port

On/Off

24V power input socket

Do not place the PDQeX close to a RF transmitter. A low power transmitter, such as a cordless or mobile phone,should be at least 2M from the PDQeX. A powerful transmitter, such as a commercial TV or radio broadcast
antenna, should be at least 25M away.
The USB port is for software upgrades only and is not to be used for other purposes.
Front of the PDQeX

Cartridge lifting tool

Hinged flap to secure cartridges

Drawer for collection tube rack

Collection tube rack

Device Set-up

05

Operating Instructions
Loading and unloading the PDQeX
The door of the PDQeX slides horizontallyleft and right. The door will lock during
operation or UV decontamination.
Before inserting any cartridges into theblock, ensure the lifting tool is in place,making it easier to remove spent
cartridges after the run is complete.

Pull out the collection tube rack and place
0.2 ml PCR tubes firmly into the rack.
The rack will accommodate up to three 8strip PCR tubes.
Remember where you have placed thecollection tubes. You will need to place thecartridges in the same position in thecartridge block.

Replace the rack into its slot in the PDQeX
and firmly push into place.

06

Loading and UnloadingOperating Instructions

Load your sample into the PDQeX
extractor cartridge.
This part of the procedure differs
depending on the sample type. The sample
may be in suspension, a solid or a disk ofstorage card.
Insert the cap into the cartridge.

Load the cartridges into the holes of the
cartridge tray in the same position where
you placed the collection tubes.
When all the cartridges are loaded, lower
the hinged flap onto the caps of thecartridges and close the sliding door.
Make sure the cartridge positions in the
cartridge tray correspond to the collection
tubes below - otherwise you willcontaminate the device.

WARNING: The lower end of the PDQeX cartridge is designed to fit inside the collector
tube. If it is above the upper lip of the tube, there is a risk of cross contamination. This
problem may occur when lower profile collection plates or tubes are used.
Contact MicroGEM at info@microgembio.com if you need a collection drawer tailored for the profileof your tubes.

Loading and Unloading07

Operating Instructions
Loading and unloading the PDQeX
After running the device, the DNA will be in
the collection tubes.
First remove the PDQeX extractor
cartridges and dispose. Slide out thedrawer.
Remove and cap the collection tubes andstore at -20° C.

Notes
The door of the device will lock while the block is hot.
For sequential runs, make sure the block temperature has fallen below the first temperature used in yourprogram.
Carefully remove tubes to prevent contamination of the block.
Tubes cannot be re-used if you abort a run.

08

Loading and UnloadingOperating Instructions
Running your program
The PDQeX is controlled by a touch-screen. The following section provides an overview to help navigate throughthe controls.

1. Home Screen
The home screen provides three options:
1. System settings
2. UV treatment (sterilization)
3. Extraction
To the left of the screen is a map to help
navigate the program.

2. System Settings
The system settings window allows you to:
1. Set date and time
2. Obtain more information
3. Reset to factory defaults
Future releases will allow you to pick yourpreferred language.

2.1 Factory Reset
The device arrives with a number of preinstalled programs. A factory reset
restores the programs if lost.
However, if you choose to reset, all custom
programs will be removed and the date andtime will need to be reset.

Running Your Program: Settings

09Operating Instructions

2.2 Date and Time
Set the date and time using the keypad andpress Save.

2.3 QR CodeThe last system option provides a QR Codeto access more information from theMicroGEM website.

3. UV Treatment
The PDQeX is fitted with four UV strip lights to reduce DNA contamination. Three lights are situated below thecollection tube drawer. The drawer should be removed before treatment to allow the light to access the lower
side of the heating block. The other light is above the heating block. During UV treatment, the sliding door will
be locked.
WARNING: Do not operate the UV light without closing the door. Avoid looking directlyat the UV light.
The UV treatment will only remove superficial contamination. For more serious spills,clean the inside of the device using a cotton swab soaked in 1% bleach. Follow this byswabbing with 80% ethanol.

10

Running Your Program: Date and TimeOperating Instructions

Press 'UV Treatment' on the home screen.
The procedure takes 30 minutes and canbe interrupted at any time.
Press Interrupt to stop the UV treatment.

After interrupting the program, press
Return to go back to the home screen.

After the treatment is complete, press
Return to go back to the home screen.

Running Your Program: UV Treatment

11Operating Instructions

4. Running Pre-defined Programs on the PDQeX
On the home screen, press Extract.
Select the program you want to run.

The temperature regimen will be shown.
Press Start.

The PDQeX will switch to a display
showing the progress of the program.
At any time, the program can beterminated but the samples and tubes
cannot be reused.
Once the run is complete, a prompt willappear to return to the extraction screen.

12

Running Your Program: Pre-definedOperating Instructions

5. Writing a Custom Program on the PDQeX
From the home screen, press Extract.
Instead of choosing one of the pre-definedprograms, it is possible to create a custom
program. This can be useful for optimizing
the PDQeX for specfic sample types.
Press the + button.

Click on the dashed line at the top of thescreen (*-----------*) and give thecustom program a name. A program
cannot be saved without a name.
Press on the temperature/time symbols( -- ) to add temperature and time values.

Use the number keypad to enter
temperature (C°) and time (minutes)
values.
Press Save. You must add a final cool step
before the program can be saved.
When you have completed all the entries
and saved the program, proceed with thesteps in section 4.

Running Your Program: Custom

13

Operating Instructions
6. Error Messages
A few common mistakes may be detected by the device.

The PDQeX has a sensor at the back of thecollection tube drawer. If the drawer is notin place or is crooked, the device will notrun.
This prevents
contaminated.

DNAfrombeing

Make sure the sliding door is fully closed
before running the PDQeX.
The block is hot and could burn fingers.

This message is a reminder that the same
tubes cannot be run twice if a run has beenaborted.

14Running Your Program: Error Messages

Cleaning, Sterilization, Inspection, and Maintenance

Cleaning and Sterilization
Collection trays and cartridge holders should be cleaned and sterilized in accordance with laboratory procedure.
The UV treatment option on the control screen gives a 30-minute UV light exposure (see pages 10-11).
In the event of gross contamination of the heating block or device, clean with a cotton swab and wipe with 0.5%
bleach followed by a thorough removal of the bleach with water-dampened swabs and wipes.
Aluminum parts of this device should not be soaked in virkon or bleach. Extended use of chemical agents suchas these will corrode the parts.
WARNING: Do not get liquids inside the device.
If bleach must be used, be sure ALL of it is removed.

Safety LabelThe following label may be displayed on the device:
Hazard Symbol

EnglishFrancaisUVWARNING: Avoid looking
directly at the UV light

AVERTISSEMENT: Évitez
de regarder directement àla lumière UVInspection and Maintenance
The PDQeX has been designed to require no operator maintenance.

Disposal of Waste
Used PDQeX cartridge tubes should be disposed as hazardous waste in accordance with laboratory protocols.

Cleaning, Sterilization, Inspection, and Maintenance15

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All trademarks are the property of their respective owners. forensicGEM*, phytoGEM*, prepGEM, RNAGEM,
and MicroGEM are trademarks in use by the MicroGEM group.
* Registered with the United States Patent and Trademark Office.
For information regarding device compliance with various agency standards, contact info@microgembio.com.

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info@microgembio.com+1-434-529-8212

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