Mapping 250K/500K SNP assay

SCANNING THE PROBE ARRAY
150 GeneChip ® Mapping 500K Assay Manual
3. Insert the cartridge into the scanner and test the autofocus to
ensure the spots do not interfere with the focus. If a focus error
message is observed, remove the spot and apply a new spot. Ensure
that the spots lie flat.
Customers using the Autoloader should refer to the Autoloader
User’s Guide.
1. Select Run → Scanner from the menu bar. Alternatively, click the
Start Scan icon in the tool bar.
The Scanner dialog box appears with a drop-down list of all
unscanned experiments.
2. Select the experiment name that corresponds to the probe array
being scanned.
A previously run experiment can also be selected by using the
Include Scanned Experiments option box. After selecting this
option, previously scanned experiments appear in the drop-down
list.
If the experiment name is not seen in the scanner dialog box, open
the workflow monitor, right-click your experiment, and select
“Advance to Scan.” Refer to the GeneChip ® Operating Software
User’s Guide for further information.
3. Click the Load/Eject button and place the array in the scanner.
Only one scan is required for the GeneChip Scanner 3000 7G.
Please do not attempt to manually open or close the GeneChip ®
Scanner 3000 7G scanner door as this may damage the scanner.
4. Once the experiment has been selected, click the Start button.
A dialog box prompts to load the array into the scanner.