Bio-Rad Components for Older Model Spot Cutter - Manual (Page 26)

Section 4
Spot Excision
4.1 Gel and Blot Preparation
• Storage of gels can be in any type of container or plastic that keeps the gel protected and
hydrated until they are needed for spot cutting. Before cutting the gel, it is best to
equilibrate the gel in water. This will avoid any swelling that may occur from water being
added to the gel on the cutting platform. 1–2 hours to overnight is sufficient to
equilibrate the gel. When equilibrating, bring the gel to room temperature if they have
been previously stored in the refrigerator. This minimizes the chances of swelling during
cutting.
4.2 Transfer of Gel or Blot to Cutting Platform
• Place the excision mat and gel cutting sheet on the cutting platform of the Spot Cutter.
• Place the gel or membrane on the gel cutting sheet. (The gel cutting sheet can be used to
transfer the gel from the storage container to the cutting platform.) Position the gel or
membrane against the right side of the cutting platform to maximize the cutting range.
• Position the Gel-holding Bars on the edges of the gel or membrane partly resting on the
cutting mat and partly resting on the edge of the gel.
• Add a sufficient amount of water to the surface of the gel to form a shallow pool (do not
fill to the top of the platform). For optimum gel cut pick up rate, make sure there is a
sufficient amount of water during the excision process.
• If the spot pickup rate is less than 95% of spots picked up first time, try less water on the
gel. Reduce the amount of water added to a film of water on the gel - enough to keep the
gel hydrated, but less than a "pool" of water. This may improve the cutting pickup rate.
For more information on improving the pickup rate, see the Troubleshooting section.
4.3 Set-up PDQuest Basic Excision Tool Software
The PDQuest software contains the Basic Excision Tool module the Basic Excision Tool
manages all the operations of the spot cutter including, image acquisition, calibration,
manual spot selection, cutter operation and data tracking. (A detailed description of the fully
integrated features with PDQuest image analysis software is discussed in the PDQuest user’s
manual.)
Open Basic Excision Tool:
•
Double click on the PDQuest icon in the desktop.
• Select the menu item "Identification", then the drop down menu item "Basic Excision
Tool".
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