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GenePix

®

4000B Microarray Scanner

User Guide

5000450 D

October 2010

GenePix_4000B.book Page 1 Friday, October 22, 2010 3:07 PM

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Summary of Contents for GenePix 4000B

Page 1: ...GenePix 4000B Microarray Scanner User Guide 5000450 D October 2010 GenePix_4000B book Page 1 Friday October 22 2010 3 07 PM...

Page 2: ...sage is intended only to designate those manufacturers products as supplied by Molecular Devices for incorporation into its equipment and does not imply any right and or license to use or permit other...

Page 3: ...HAT HAVE INTELLECTUAL PROPERTY RIGHTS IN THE POTENTIAL FIELD OF APPLICATION OF THIS INSTRUMENT INCLUDE WITHOUT LIMITATION AFFYMETRIX INC AFFYMETRIX AGILENT AND OXFORD GENE TECHNOLOGY THIS INSTRUMENT H...

Page 4: ...4 5000450 D GenePix_4000B book Page 4 Friday October 22 2010 3 07 PM...

Page 5: ...h 13 Installing the Software 16 Turning on the Scanner 17 Inserting a Slide 17 Shutting Down the Scanner 19 Chapter 3 Maintenance Troubleshooting 21 Moving the Scanner 22 Interlock Failure Symptoms 23...

Page 6: ...6 5000450 D Appendix C Warranty and Service 33 Standard Warranty 33 Out of Warranty Repair Service 33 Optional Service Agreement 33 Technical Support 34 GenePix_4000B book Page 6 Friday October 22 201...

Page 7: ...that can cause damage to the instrument device or data if precautions are not followed Related Documentation The customer documentation for the GenePix 4000B Microarray Scanner includes the GenePix P...

Page 8: ...Foreword 8 5000450 D GenePix_4000B book Page 8 Friday October 22 2010 3 07 PM...

Page 9: ...o internally installed laser excitation sources A user attenuated lasers allowing 10 33 and 100 transmission Simultaneous scanning of two wavelengths User adjustable focus Precisely controlled automat...

Page 10: ...are Protective enclosure Optics Lasers Optical path Emission filters PMTs photo multiplier tubes Status lights External power supply Figure1 1 GenePix 4000B Microarray Scanner For detailed information...

Page 11: ...tector Dual PMTs Signal digital output 16 bit Image format Single or multi image TIFF Computer interface USB 2 0 Scan time 6 5 minutes at 10 m resolution Dynamic range Four orders of magnitude Uniform...

Page 12: ...t 50 to 60 Hz 100 to 240 VAC 2A max Space 25 6 inches deep by 16 9 inches wide by 13 4 inches high 65 cm by 43 cm by 34 cm An additional 6 inches 15 2 cm for clearance Bench support Sufficient to supp...

Page 13: ...ires repair you must return it in the original packaging If the crate has been damaged in transit you must retain it for inspection by the carrier WARNING Shock Hazard In an emergency users must be ab...

Page 14: ...m direct sunlight dust drafts vibration and moisture Carefully move the scanner to its final position 3 Plug the USB cable into the USB type B port on the back of the scanner and the USB type A port o...

Page 15: ...and the lab s power outlet We recommend you use a surge protector between the main power cable and the power outlet Figure2 2 Main power supply cable components Item Name Description 1 Round connector...

Page 16: ...stall the GenePix Pro Software CAUTION Do not to insert the security key into the control computer until after the GenePix Pro Software has been installed 4 Install the security key For more informati...

Page 17: ...ware performance events into the Hardware Diagnostics Report every two hours during operation Inserting a Slide The slide holder is a precision component designed to ensure proper focusing and field u...

Page 18: ...r the top of the slide holder Note Make sure the barcode on the slide is facing the front of the scanner Figure2 3 Slider holder Ite m Name Description 1 Slide door In open position 2 Slide holder In...

Page 19: ...hutting Down the Scanner Proper shutdown of the GenePix 4000B Microarray Scanner ensures the scanner or software are not damaged To shut down the scanner 1 Close the GenePix Pro Software 2 Turn off th...

Page 20: ...Installation and Operation 20 5000450 D GenePix_4000B book Page 20 Friday October 22 2010 3 07 PM...

Page 21: ...re returning the scanner or any components WARNING Biohazardous Material Never perform any maintenance procedures on the scanner in an environment where potentially damaging gases or liquids are prese...

Page 22: ...enePix Utilities The GenePix Utilities window appears 4 Click Park Scanner for Shipping A message box appears informing you that the scanner has been successfully parked CAUTION Always turn off power...

Page 23: ...e 4000B Microarray Scanner Shut down the scanner and contact Technical Support immediately The following are typical symptoms of an interlock failure The mirror and lens assembly keep moving below the...

Page 24: ...50 D Fuses If the GenePix 4000B Microarray Scanner does not start up a fuse might no longer be functioning If you suspect a fuse has stopped functioning contact Technical Support GenePix_4000B book Pa...

Page 25: ...similar fluorescent characteristics The individual lasers have been selected because of their superior optical performance and reliability Since the performance of such lasers is often sensitive to e...

Page 26: ...croarray Scanner employs two approaches to reduce crosstalk to negligible levels First the filter sets and excitation lasers have been carefully chosen to ensure that crosstalk between the two fluorop...

Page 27: ...e range of incident light intensities However there is a very non linear relationship between the voltage of the PMT and the PMT output Therefore a slide scanned at a PMT voltage of 800 V will not be...

Page 28: ...Eject FigureA 1 Status lights GenePix 4000B Microarray Scanner Item Color Name Description 1 Green Device standby The scanner is powered up and ready to scan a slide 2 Blue Scanning The slide is in th...

Page 29: ...ne by increasing each Y direction step from 5 m to 10 m Consequently a 10 m scan is twice as fast as a scan at 5 m and outputs the average of each adjacent pair of 5 m spots in the X direction as the...

Page 30: ...ation of how the GenePix 4000B Microarray Scanner samples 5 m spots and averages them to calculate the values of the image pixels for the various scan modes and pixel sizes On the left side of each im...

Page 31: ...he gain is set below this range the probability that each impinging photon will be converted to an electron is diminished and the dynamic range will be limited on the low end Above this range noise be...

Page 32: ...Instrument Performance Factors 32 5000450 D GenePix_4000B book Page 32 Friday October 22 2010 3 07 PM...

Page 33: ...ducts returned to Molecular Devices for repair should be properly packaged with transportation charges prepaid Molecular Devices will pay for the return shipping of the product to the customer If the...

Page 34: ...ur name you can then register your instrument If you require advice on the use of your GenePix 4000B Microarray Scanner do not hesitate to contact Molecular Devices Technical Support Visit the website...

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