pdf,677 KB - Thermo Fisher Scientific

pdf,677 KB - Thermo Fisher Scientific
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
same as Run→
1. On the back of the probe array cartridge, clean excess fluid from around
2. Carefully apply
one Tough-Spot
over each of the
two septa. Press
to ensure that
the spot remains
flat. If the
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
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.
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
or from
USA Scientific, Inc. P.O. Box 3565 Ocala, FL 34478 (800)LAB-TIPS P/N 9185-0000
Initial boot up
Scanner boot up
Laser warm up
Scanner in error
System is ready
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
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
Note: A new experiment
must be opened for each
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
5. Repeat steps 1 to 4 until
all of the probe array
cartridges have been
Manually Extracting a Probe Array Cartridge
If your probe array
cartridge becomes stuck
in the scanner, remove
the cartridge in the
following steps.
1. Shut down the
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.
Santa Clara, CA 95051 USA
Wycombe Lane, Wooburn Green,
4-1-23 Shiba, Minato-ku
3380 Central Expressway
Tel: 1-888-362-2447
Fax: 1-408-731-5441
[email protected]
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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