Proper Use of Tough-SpotsTM To Prevent Leaking Before scanning the probe array cartridge, follow this procedure to prevent the leaking of fluids from the cartridge during scanning. Opens the Station Selection and Fluidics Station dialog box (the →Fluidics). same as Run→ 1. On the back of the probe array cartridge, clean excess fluid from around septa. 2. Carefully apply one Tough-Spot over each of the two septa. Press to ensure that the spot remains flat. If the Tough-Spot does not apply smoothly; that is, if you observe bumps, bubbles, tears or curled edges, do not attempt to smooth out the spot. Remove the spot and apply a new one. Inserting a GeneChip® Probe Array Cartridge GCOS Instrument Control Shortcut Bar →Start Scanner). Opens the Scanner dialog box (the same as Run→ Scanner Indicator Lights Three lights on the front panel of the scanner indicate the scanner’s various states. TM Tough-Spots At the software prompt, insert the GeneChip® probe array cartridge into the chip transport unit and seat snugly as shown on the right. The front of the probe array cartridge (the white label side) must be facing the rear of the scanner. Scanning a Probe Array 1. Click the Scanner button in the Instrument Control shortcut bar or in the →Start Scanner The Scanner dialog box opens. main toolbar, or click Run→ 2. If the scanner is in sleep mode, click the Turn Laser On button and wait 10 minutes for the laser to warm up. When the laser is ready, the Start and Load/Eject Chip buttons will highlight. 3. To include scanned experiments in the Experiment Name drop-down list, choose the Include Scanned Experiments option. 4. Select the experiment name of the probe array to be scanned from the Experiment Name drop-down list. 5. To average several scans, type in the number of Scans for this experiment. 6. Click Start in the Scanner dialog box. The scanner options window opens. 7. Load the probe array in the scanner as prompted and click the OK button. The scanner door will close itself and a scan will commence. 3. Insert the cartridge into the scanner and begin scanning. If you observe a focus error message, remove the cartridge and remove the spot and apply a new spot. Ensure that the spots lie flat. Note: Apply new spots just before scanning. Do not use the same spots that may have been used during the overnight hybridization or applied after fluidics washing. Also: To reduce the risk of leakage, do not use excessively large pipette tips to apply solution to pierce the septa. Affymetrix recommends the use of Tough-Spots™ obtained from Affymetrix P/N 64-0158 Green Yellow Blue Indication or from USA Scientific, Inc. P.O. Box 3565 Ocala, FL 34478 (800)LAB-TIPS P/N 9185-0000 OFF OFF ON Initial boot up ON ON ON Scanner boot up OFF ON ON Laser warm up OFF Flashing ON Scanner in error ON OFF ON System is ready Flashing OFF ON Scan in progress Starting the GeneChip® Scanner 3000 7G Press the I/O button to turn on the scanner; the laser automatically is turned on. The laser takes 10 minutes to warm up and stabilize. During the initial power up (CPU boot up), both the green and yellow lights will be off. During the scanner boot up, both the green and yellow lights will be on. Scanner dialog box, laser off (left) and laser on (right) Note: If the scanner has entered Park state with a probe array cartridge still in the Chip Transport Mechanism, press the Eject Chip button to raise the cartridge from the scanner. Stopping a Scan →Stop Scanner from the 1. Click the Stop toolbar button or select Run→ menu bar. 2. At the prompt, click Yes to stop the scanner or No to resume scanning. 3. If you click Yes, you will lose the data from a partial scan. This is different from earlier software versions where you could save the data from a partial scan as a .dat file. 4. After you stop a scan, the scanner will automatically eject the chip. Caution: If you stop the scanner while a probe array is in the process of scan ning, you will lose all scan information from that probe array. If you rescan the array, it may be affected due to uneven photo-bleaching. This could potentially make the data from the array difficult to compare to other array data. Shutting Down the Scanner 1. Close the GCOS software. This is the best way to shut off the laser. 2. Press the I/O button on the front panel to turn off the instrument. Scanning the Cartridge Barcode 1. Open the GeneChip® Operating Software (GCOS) to the Experiment Information window and place the cursor in the Barcode field. Note: A new experiment must be opened for each barcode. 2. Hold a GeneChip probe array cartridge in front of the barcode reader. 3. Squeeze the trigger until you hear a beep. The reader reads and sends the barcode to the GCOS Experiment Information window, Barcode field. 4. After the software adds the barcode, save the experiment. 5. Repeat steps 1 to 4 until all of the probe array cartridges have been read. Manually Extracting a Probe Array Cartridge VERSION B If your probe array cartridge becomes stuck in the scanner, remove the cartridge in the following steps. 1. Shut down the scanner. 2. Insert a paper clip or small Allen wrench into the rescue hole on top of the scanner and press to partially lift the cartridge loading door. 3. Using your fingers, gently lift the front edge of the door. As you lift the front edge, lift the back edge approximately 1/4” to open the door straight up to expose the rescue screw in the front. 4. Using a standard (-) screwdriver, turn the screw in a clockwise direction until the probe array cartridge ascends, then grab the cartridge and lift it out. 5. Rescrew the chip transport mechanism. Note that the screw is fine pitched and requires a number of turns. Stop if you encounter screw resistance. Do not over torque. AFFYMETRIX, INC. AFFYMETRIX, UK Ltd. AFFYMETRIX, JAPAN K.K. Santa Clara, CA 95051 USA Wycombe Lane, Wooburn Green, 4-1-23 Shiba, Minato-ku 3380 Central Expressway Tel: 1-888-362-2447 (1-888-DNA-CHIP) Fax: 1-408-731-5441 [email protected] www.affymetrix.com P/N 08-0182 Rev. B For Research Use Only Voyager, Mercury Park, High Wycombe HP10 0HH United Kingdom Tel: +44 (0) 1628 552550 Fax: +44 (0) 1628 552585 [email protected] Not For Use In Diagnostic Procedures Mita NN Bldg 16 Floor Tokyo 108-0014, Japan Affymetrix GeneChip® Scanner 3000 7G Quick Reference Card Tel: +81-(0)3-5730-8200 Fax: +81-(0)3-5730-8201 [email protected] ® ® ® © 2005 Affymetrix, Inc. All rights reserved. Affymetrix®, GeneChip®, , , , EASI™, HuSNP®, GenFlex®, Flying Objective™, Jaguar™, CustomExpress®, NetAffx™, CustomSeq™, “Tools To Take You As Far As Your Vision®” and “The Way Ahead™” are trademarks owned or used by Affymetrix, Inc. This card provides you with a quick tour of the operation of the GCS3000 7G.
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