GENOMICS and SEQUENCING CENTER

QIAcube – Standard Operating Procedure

Automated Sample Processing

Purpose

Performs fully automated processing of up to 12 samples.

Purification: genomic DNA, plasmid DNA, RNA, viral nucleic acids, proteins
Cleanup: DNA, RNA

The user selects a preset protocol using the touchscreen, and loads plasticware, samples, and reagents
onto the QIAcube worktable. The user closes the instrument and starts the protocol, which
provides all the necessary commands for sample lysis and purification using QIAGEN spin
columns. A fully automated load check helps to ensure correct loading.

Sample preparation using the QIAcube follows the same steps as the manual procedure using standard
QIAGEN spin column kits. The QIAcube uses special 1.5 ml and 2 ml tubes not provided in the
kits.

For detailed information refer to the QIAcube User Manual.

I. QIAcube Protocols

All QIAcube protocols can be downloaded free of charge at www.qiagen.com/MyQIAcube. Prior to

use, a PDF of the specific protocol to be used should be downloaded and printed by the user. Refer to
the handbook supplied with the QIAGEN kit you are using and the relevant protocol sheet to find out
which protocol to load and to obtain further details about the protocol. The PDF contains
information regarding accessory reagents, tube setup, and any other additional information.

The QIAcube instrument can only store 10 protocols. If necessary, protocols can be uploaded from
the QIAcube USB stick. Prior to use the user should check to ensure that their protocol has been stored
on the QIAcube. If the protocol has not been stored, a GSC employee will download the necessary
protocol from www.qiagen.com/MyQIAcube and upload it to the QIAcube.

Certain parameters within specific protocols can be edited, i.e. elution volumes. Saving the protocol
after editing will overwrite the default protocol. Users should check all parameters of the protocol
before starting.

II. QIAcube Operating Procedures

1. Carefully read the QIAGEN kit handbook and the relevant protocol sheet.

2. Prepare and load the samples and reagents to be used in the protocol. Follow the specific protocol
and the QIAcube Loading chart.

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3. Select the appropriate application from the main menu by pressing “CLEANUP”, “DNA”, “RNA”,
“PROTEIN”, OR “VIRUS”.

4. Select the correct kit name by pressing “” or “” to scroll through the list until the correct kit name
is highlighted, and then press “Select”.

5. Select the sample material (this step may not be required for all protocols).

6. Depending on the protocol, further options may be available (e.g., standard protocol,
homogenization using a QIAshredder column, on-column DNase digest, etc.). Scroll through the list
until the required protocol is highlighted.

7. Press “START”

8. To enter user-defined values for certain parameters such as elution volume, press “EDIT”. Not all
protocols allow user-defined values to be entered.

9. Change values by pressing “”, “”, or “DEFAULT”. Press “SAVE” to save changes, then “BACK”
to exit edit mode.

10. Press “Start” to begin.

11. Follow the instructions in the protocol sheet and displayed in the touchscreen for loading the
worktable with samples, reagents, and labware. You will be instructed to:
 Empty the waste drawer.
 Place appropriate tip racks onto the worktable. Tip racks snap into place and should not
be forced.
 Fill the reagent bottles and place the reagent bottle rack onto the worktable. Be sure to
remove lids from reagent bottles before placing on the worktable.
 Load opened accessory buffer tubes required by the protocol in positions A, B, or C.
 Place the loaded rotor adapters into the centrifuge buckets. Follow the diagram on the
protocol for proper rotor adapter loading. If your protocol requires you to cut the cap
off of a tube, you must cut it off completely, without leaving any excess plastic that
will interfere with the robot arm.
 Load the shaker rack with samples, and place onto the shaker. Be sure to use the correct
sample tubes and the correct shaker adapter, as described in the protocol sheet.
QIAGEN supplies both 1.5 ml elution tubes and 2 ml sample tubes for the QIAcube.

12. Close the instrument door. The door of the QIAcube must remain closed during operation of the
instrument. Only open the door when instructed to do so by the software.

13. After you have set up the worktable, the QIAcube performs a load check:
 The instrument is initialized
 The shaker is checked to make sure it is correctly loaded.
 The number of rotor adapters in the centrifuge is checked to make sure that it corresponds to
the number of samples in the shaker and that the rotor is correctly loaded.

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  The reagent bottle rack is checked to make sure that it is correctly loaded and there is
sufficient buffer in the reagent bottles.

NOTE: The volume of accessory buffers in positions A, B, or C is not checked. Be sure to

fill accessory buffers with the exact volume noted on the protocol sheet.
 The filter-tips are checked to make sure that the correct type has been loaded and that there
are sufficient filter-tips for the protocol run.

14. If the load check is unsuccessful, an error message will be displayed in the touchscreen. Resolve the
error so that the protocol run can continue. Only move or change the affected samples or labware.
Refer to the QIAcube User Manual troubleshooting section for more details on error messages. If
you have an error message that cannot be easily rectified, please see the GSC manager for
assistance. Do not attempt to service the QIAcube.

15. When the protocol run has finished, a message is displayed in the touchscreen confirming that the
samples have been processed. Follow the instructions in the touchscreen for worktable cleanup:
 Remove the microcentrifuge tubes containing purified nucleic acids or proteins from the
rotor adapters.
 Empty the rotor adapter waste into the appropriate container.
 Discard sample tubes, used rotor adapters, and reagents.
 Return the regents back to their original containers or replace lids on reagent bottles.
 Empty the waste drawer.

16. You can stop a QIAGEN protocol by pressing “CANCEL”. If a protocol run is stopped, the run
cannot be restarted and samples must be processed manually.

17. Please record your use in the logbook.

[Created by Maureen Varina; June, 2009]