Bio-Rad EXQuest Spot Cutter - Manual (Page 40)

Figure 5-5. Import excision coordinate list.
3. If the first line of your file is header information, check Skip first line of file.
4. Enter the column number in which the coordinates are located. For example, if your file lists the spot
number in column one, the X coordinates in column two and Y coordinates in three, then you would
enter 2 for column X and 3 for column Y. Columns must be separated by tabs or by columns.
5. Click the browse button, "…", to locate the coordinate file to import.
6. Select the appropriate coordinate measurement unit in the Units field.
7. Select the coordinate system origin: Upper left or Lower left.
8. Once all the correct information has been supplied, orange cut marks will appear on the gel image.
Click the mouse and drag all the cut marks, as a group, to better position them on the gel.
9. Click Done to accept the cut mark locations. After you have accepted the cut requests, you may
move individual cuts using the Add/move cut function.
10. Continue setting up the cut run as described in Section 5.1, Step 14.
5.3 CONFIRM CUTS
The Confirm cuts function is used to identify missed gel spots and is particularly useful for fluorescent
stained gels since the clear gel spots (with no visible stain) are difficult to see in microplate wells. The
confirm cuts function can be used to image microplates to locate wells that do not have gel plugs in them, or
to image gels to locate gel plugs that have not been picked up. Its use is optional and generally not required
due to the EXQuest spot cutter's high cutting efficiency.
5.3.1 Identifying Re-cuts from a Microplate Image
1. The "Confirm cuts?" pop-up box automatically appears at the end of a cut run (see Figure 5-6,
below) when the gel has been imaged with the "UV EPI" light. Click Yes to acquire an image of the
microplates or No to return to the "Manual Excision Tool" window.
MANUAL EXCISION TOOL
5-5