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Introduction

5001410 B

Applications of the GenePix SL50 Slide Loader

The GenePix SL50 Slide Loader can be used for numerous applications

related to the individual and batch processing of microarray slides,

including, but not limited to:

•

Gene expression arrays

•

Protein arrays

•

Arrayed comparative genomic hybridization (aCGH) arrays

•

Chromatin immunoprecipitation (ChIP) arrays

•

DNA methylation arrays

•

SNP genotyping arrays

•

RNA interference (RNAi) arrays

•

MicroRNA (miRNA) arrays

Specifications of the GenePix SL50 Slide Loader
and GenePix 4300A/4400A Microarray Scanner

Figure 1-1

GenePix SL50 Slide Loader and GenePix 4300A/4400A

Microarray Scanner Specifications

Specification

Measurement

Weight (GenePix SL50 Slide Loader)

41 kg

Weight (GenePix 4300A/4400A scanner)

45 kg

Combined Weight

86 kg

Combined Height

620 mm

Combined Width

807 mm

Combined Depth

870 mm

Mains Power Input

100V - 240 VAC, 125W

Mains Voltage Fluctuations

Not to exceed 10% of nominal

supply voltage

Equipment Class

Pollution Degree

Installation Category

Operating Environment

Indoor Use Only

Altitude

Not to exceed 2000 m

Operating Temperature

5 - 40 degrees C

Humidity

< 80% RH at 40 degrees C

GenePix SL50.book Page 10 Tuesday, February 1, 2011 12:20 PM

Содержание GenePix SL50

Страница 1: ...GenePix SL50 Slide Loader User Guide 5001410 B February 2011 GenePix SL50 book Page 1 Tuesday February 1 2011 12 20 PM ...

Страница 2: ...usage 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 others to use such manufacturers and or their product names as trademarks Molecular Devices makes no warranties or representations as to the fitness of this equipment for any particular purpose and assume...

Страница 3: ...ertheless researchers should independently verify the basic accuracy of the slide loader using suitable test samples WARNING If this equipment is used in a manner not specified by the manufacturer the protection provided by the equipment may be impaired DISCLAIMER This equipment is not intended to be used and should not be used in human experimentation or applied to humans in any way GenePix SL50 ...

Страница 4: ...PROPERTY RIGHTS IN THE POTENTIAL FIELD OF APPLICATION OF THIS INSTRUMENT INCLUDE WITHOUT LIMITATION AFFYMETRIX INC AFFYMETRIX AGILENT AND OXFORD GENE TECHNOLOGY THIS INSTRUMENT HAS NOT BEEN LICENSED OR APPROVED FOR DIAGNOSTIC APPLICATIONS THE USE OF THIS INSTRUMENT IN CONNECTION WITH MICROARRAYS MAY BE WITHIN THE SCOPE OF PATENTS HELD BY AFFYMETRIX TO THE EXTENT THAT AFFYMETRIX PATENT RIGHTS ENCOM...

Страница 5: ... Canada ICES NMB 001 2006 13 ISM Equipment Classification Group 1 Class A 13 Information to the User FCC Notice 13 Chapter 2 Operation 15 Operation Startup Procedure 15 Turning on the control computer 15 Turning on the scanner 15 Turning on the slide loader 16 Starting the GenePix Pro Software 16 GenePix Pro Software icons 16 Performing a Functional Checkout 18 Manual Scanning 20 Batch Scanning 23...

Страница 6: ...ing Particles from Equipment 32 Troubleshooting Fuse Errors 32 Returning the Slide Loader to Home Position 33 Appendix A Warranty and Service 35 Standard Warranty 35 Out of Warranty Repair Service 35 Optional Service Agreement 35 Technical Support 36 GenePix SL50 book Page 6 Tuesday February 1 2011 12 20 PM ...

Страница 7: ... data if the precautions are not followed Related documentation The customer documentation for the GenePix SL50 Slide Loader includes the GenePix 4300A 4400A User Guide the GenePix Pro 7 Software User Guide and the GenePix Pro online Help WARNING Indicates an operation that may cause personal injury if precautions are not followed Tip Provides useful information that helps apply the techniques and...

Страница 8: ...Foreword 8 5001410 B GenePix SL50 book Page 8 Tuesday February 1 2011 12 20 PM ...

Страница 9: ...pping Slide cassette detection Manual single slide scanning capability independent of the automated mechanism 3 axis robotic slide assembly for moving slides from slide storage to the scanner and back Support for Auto PMT on all scan areas for individual slides Accommodation of standard 1 inch by 3 inch 25 mm by 75 mm microscope slides Audible noise of less than 70 dB during operation Direct commu...

Страница 10: ...lide Loader and GenePix 4300A 4400A Microarray Scanner Figure1 1 GenePix SL50 Slide Loader and GenePix 4300A 4400A Microarray Scanner Specifications Specification Measurement Weight GenePix SL50 Slide Loader 41 kg Weight GenePix 4300A 4400A scanner 45 kg Combined Weight 86 kg Combined Height 620 mm Combined Width 807 mm Combined Depth 870 mm Mains Power Input 100V 240 VAC 125W Mains Voltage Fluctu...

Страница 11: ...he slide loader in an environment where potentially damaging gases or liquids are present WARNING Shock Hazard Do not remove the protective enclosure or any covers marked with the high voltage warning symbol WARNING Shock Hazard Always turn the power switch off and disconnect the main power cable before performing any maintenance procedures WARNING Shock Hazard The GenePix SL50 Slide Loader is an ...

Страница 12: ...G Pinching hazard To avoid potential injury use caution when working near a potential pinch hazard location WARNING Lifting hazard The slide loader weighs approximately 90 pounds 41 kg and is precisely aligned to the scanner To avoid potential injury and potential damage to the alignment and equipment contact Molecular Devices if you need to move the slide loader This symbol indicates that you mus...

Страница 13: ...ance with FCC regulations shielded cables must be used with this equipment Operation with non approved equipment or unshielded cables can result in interference to radio and TV reception This equipment generates uses and can radiate radio frequency energy and if not installed and used in accordance with the instructions can cause harmful interference to radio communications There is no guarantee t...

Страница 14: ...Introduction 14 5001410 B GenePix SL50 book Page 14 Tuesday February 1 2011 12 20 PM ...

Страница 15: ...er on page 15 Turning on the scanner on page 15 Turning on the slide loader on page 16 Starting the GenePix Pro Software on page 16 Turning on the control computer Molecular Devices service personnel will install and set up the slide loader and scanner and connect them to a control computer where the GenePix Pro Software is installed To turn on the control computer Turn on the control computer pow...

Страница 16: ...urn on the slide loader power switch The power LED turns on No movement occurs 4 If this is the first time you are turning on the slide loader or if you want to check the performance of the instrument go to Performing a Functional Checkout on page 18 Starting the GenePix Pro Software While it is recommended that you perform a functional checkout after initial installation of the GenePix SL50 Slide...

Страница 17: ...x Pro Software icons Icon Description Scan Area Properties Scanner Door is Open Click to Close Scanner Door Scanner Door is Closed Click to Open Scanner Door Hardware Settings Preview Scan Data Scan Stop Scan GenePix SL50 book Page 17 Tuesday February 1 2011 12 20 PM ...

Страница 18: ... slides that might be remaining on the slide holder from a previous session Failure to remove slides can damage the slide scanner or slide loader 3 If you are changing from Manual mode to Batch Scan mode and the GenePix Pro Software prompts you to remove any slides in the slide loader click OK Performing a Functional Checkout Use the Functional Checkout procedure to help you confirm that your Gene...

Страница 19: ...ake sure that Batch is the selected scan type If Manual is the selected scan type click Select select Batch remove any slides on the scanner s slide holder and click OK 3 On the slide loader open the slide enclosure door and remove both the left and right slide cassettes 4 Place four compatible slides in slide cassette positions 1 25 26 and 50 For more information see Using Compatible Slides on pa...

Страница 20: ...during operation Manual Scanning In Manual scan mode the GenePix Pro Software operates the scanner only in a conventional way You can open and close the motorized scanner door perform Preview Scans Data Scans adjust scanner settings from the Hardware Settings dialog box and stop and start scans Any Global file options Save locations File name set during a batch scan apply when performing a manual ...

Страница 21: ... while it is moving Never force the slide holder closed or apply significant pressure to it 2 With the slide held between your thumb and finger carefully place the slide feature side down into the slide holder Note Make sure the barcode on the slide is facing the front of the slide scanner Figure2 1 Scanner slide holder Ite m Name Description 1 Scanner door In raised position 2 Slide holder In loa...

Страница 22: ...hand side of the GenePix Pro window 5 In the Hardware Settings dialog box set the filter and PMT parameters 6 Click the Preview Scan icon to scan the slide and display general data for the slide 7 If you want to scan a smaller region use the Scan Region tool to select a region then click the Data Scan icon 8 When you are finished scanning click the Open Close Scanner Door icon 9 Remove the slide f...

Страница 23: ... slide cassettes in the slide enclosure and will not start a scan if no slide cassettes are present Only those positions containing slides are accessed during the scan On the Batch Scan tab you can customize various settings For each slide in the slide carrier you can specify hardware scanner settings and analysis settings For the entire batch scan you can specify file naming and saving options as...

Страница 24: ... To load the slide cassette 1 Use the handle on the right side of the slide loader tower to slide open the slide enclosure door Figure2 2 Slide enclosure door handle GenePix SL50 book Page 24 Tuesday February 1 2011 12 20 PM ...

Страница 25: ... When you have placed all slides for scanning into the slide cassette return the cassette to the slide enclosure by inserting it at a slight angle tilted away from you then straighten it until it fits securely in the slide enclosure You will hear a click when it is in place 5 If additional slots are required perform Step 2 through Step 4 with the right slide cassette CAUTION Do not access the slid...

Страница 26: ...sitions in gray indicate that a slide is present but has not been selected to be scanned based on the current GenePix SL50 Slide Loader settings By default all slides present in a batch are scanned 2 Click the Hardware Settings icon on the right hand side of the GenePix Pro window 3 In the Hardware Settings dialog box select the laser and filter settings for all slides To override these hardware s...

Страница 27: ... want to select a sub batch of slides for scanning use Ctrl click and Shift click to select multiple slides in the Batch Scan table and then select the following settings for the sub batch scan in the For the selected sub batch of slides group Click the Scans drop down list to select the type of scan to perform on the selected sub batch of slides Type a File name body to save the selected sub batc...

Страница 28: ... file name click Save loader settings and enter a new file name 12 Click Scan Batch to perform a batch scan using the settings configured on the Batch Scan tab When the batch scan is complete a message appears in the GenePix Pro Software Stopping a Batch Scan You can stop a batch scan at any time during the scan You can then choose to continue the scan or to cancel it To stop the current scan 1 In...

Страница 29: ... List GAL or GenePix Settings GPS file for analysis For more information on batch analysis see the GenePix Pro online help Locate the Batch Analysis topic in the GenePix Pro Features section Reviewing the Batch Scan Log File The GenePix Pro Software saves a log file for each batch of slides that it scans If there is a problem with a batch you should open and review the log file for diagnostic info...

Страница 30: ... Loader ensures that the slide loader and software are not damaged To shut down the slide loader 1 Close the GenePix Pro Software 2 Turn off the slide loader power switch 3 Turn off the scanner power switch 4 Turn off the control computer GenePix SL50 book Page 30 Tuesday February 1 2011 12 20 PM ...

Страница 31: ...de cassette can accommodate slides that are between 0 9 mm and 1 1 mm thick including any labels Slides thicker than 1 1 mm will not fit properly in the slide carrier and can cause slide handling failure because of the manual force required to remove the slides from the cassette Make sure that slides move freely in the slide cassette when you insert them Slides thinner than 0 9 mm will not remain ...

Страница 32: ...tails Removing Particles from Equipment Periodically check both the scanner and the slide cassettes for glass slide particles that can accumulate over time Use only a brush or vacuum to remove particles Do not use an aerosol duster to remove particles because this can distribute particulates to other areas of the scanner and this can result in airborne particles that can cause eye and nose irritat...

Страница 33: ...uring the procedure To return the slide loader to Home position 1 Close the GenePix Pro Software 2 Start the GenePix Pro Software 3 If a slide remains in the motion arm when the slide loader has moved to its far right position turn off the slide loader power switch and then carefully remove the slide from the gripper After removing the slide from the gripper turn on the slide loader power switch 4...

Страница 34: ...Routine Maintenance and Troubleshooting 34 5001410 B GenePix SL50 book Page 34 Tuesday February 1 2011 12 20 PM ...

Страница 35: ...ional charge Products returned 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 shipment is to a location outside the United States the customer is responsible for all duties taxes and freight clearance charges The warranty is valid when the product is used for its intended purpose an...

Страница 36: ...our name you can then register your instrument If you require advice on the use of your GenePix SL50 Slide Loader do not hesitate to contact Technical Support Visit our Technical Support web site at http support moleculardevices com and complete the Technical Support Request form You can also phone Technical Support at 1 408 747 1700 or 1 800 635 5577 USA only or 44 118 944 8000 EU Follow the prom...

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