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CapitalBio PersonalArrayer 16 user manual

1. as 0 3 microns CapitalBio Corporation 2 PersonalArrayer 16 Prologue Technical Support The staff at CapitalBio is always ready to help with any problems you may encounter with installation operation software and any related field for this instrument We also appreciate any suggests or comments you may have Contact information is as follows Address CapitalBio Corporation 18 Life Science Parkway Changping District Beijing 102206 China Tel 86 10 80725793 Fax 86 10 80726782 Website http www capitalbio com Email techsupport capitalbio com globalsales capitalbio com To ensure the best technical support please be prepared to provide the following information The SERIAL NUMBER of your CapitalBio PersonalArrayer 16 located on the nameplate at the back of the instrument The version number of the application software Description of the problem Methods you have already tried to solve the problem Your phone number fax number e mail address or any other means by which we can contact you In addition convenient access to your CapitalBio PersonalArrayer 16 during a technical support phone call will facilitate the process Additional information can be found in the following CapitalBio Corporation Documentation provided with the computer workstation and its software 3 PersonalArrayer 16 Safety Precaution Safety Precaution Warning Use of controls or adjustments
2. 1 D10 S18 QC18 1 B15 S19 QC19 1 C15 S20 C20 1 D15 S21 QC21 1 B14 S22 QC22 1 C14 S23 QC23 1 D14 S24 QC24 K o z z vio A 49 PersonalArrayer 16 Chapter 5 Slide Spotting The Sample Flag File can be an excel document or a simple text file in the specific format as described below Plate334_1 Ls Le 7 s oJioJufisfopiupis 16 17 18 22 23 24 L Fra EE GE G GE TT e G DG Ban mn na 19973 DTD DEB EA HD CO HD E E E sae DD sau 9 GOGO TD E S O A a A Pe a G AE A Sn 19 20 21 me E TE Li FE Fs nF PE GC ED Eme Segre EO ola 9307 0302 0060 DTO 0205 1347 DZD 071 S O META E G CE ooo oe eee fe E S EA EA S CDe E EE 05606 00 5 kii EEEE S A RR D amame AA CHENE EM PF MA m poe 2 E 22 23 24 29 020 020 070 020000 essa 025 rast 0208 000 0209 0052 050 005 9 Z S ramo zea ss os K a The Sample Flag File is organized in the form of a group of Sample Information Passages The Sample Information Passage should begin with a Plate Identifier which is composed of the Plate384 or Plate96 followed by the plate index When the file is loaded the program will look for a matching plate according to its type and index No The Sample Information Passage is a table of 16 rows and 24 columns referring to the 384 well plate Each column of the table in the Sample Information Passage should be separated
3. 1 8 Switch between Spotting and Dispensing Mode Users can conveniently change the Spotting Module to the Dispensing Module on the Z axis in order to switch the instrument between Spotting and Dispensing mode The procedure is as follows Step 1 Turn to the Prepare page click the Load Pin button and the Robotic Arm will move to a proper position for following operation Step 2 Use tweezers to remove Pins from the Pin Holder Step 3 Use a screwdriver to unscrew the bolts on the casing and remove the casing Step 4 Unscrew the bolts on the Pin Holder and remove them Step 5 Hold the Nozzle Holder to mount and fix it Step 6 Use a level indicator to make sure the Nozzle Holder and Platform are parallel CapitalBio Corporation 16 PersonalArrayer 16 Chapter 1 Hardware Installation Step 7 Plug in control cables and conduits Step 8 Assemble the Nozzle and fasten the bolt Step 9 Mount the casing and fasten it Step 10 Exit the application software and launch it again Step 11 Check the interface to confirm that the program has identified the hardware configuration and initialized the instrument in the Dispensing mode correctly The procedure to replace the Dispensing Module for the Spotting Module is similar Note Remove the Pin s or Nozzle before you switch the modules Expel any possible dust or particles within the air course before you assemble th
4. 1 G13 1 614 1 H4 1 H4 1 09 1 H5 1 05 1 H5 1 H6 1 H6 1 06 1 H7 1 05 1 H7 MM c20 1 20 1 H10 1 H11 1 H11 1 H11 1 012 1 H12 1 H12 1 H13 1 H13 1 H13 1 H14 1 H14 Ml o 1 09 1 H17 11 417 1 H18 1 H18 1 H18 1 H19 1 H19 1 H19 1 H20 1 H20 1 H20 1 H21 MY ia 1 015 LIS 1 5 1 15 1116 1 16 ie 11 17 11 17 14 17 1 18 ite 1 18 B 2 1x21 1 11 1 02 1 02 1 02 1 03 1 3 1 13 1 14 1 14 1 14 is ius Ml 19 i 1 18 1 18 1 119 1 119 1 119 14120 14120 1 120 1 121 1 121 1 121 11 122 Ml is 1 116 1 K6 1 6 1 K6 1 K7 1 K7 1 K7 18 18 1 K8 1K9 1 9 1 9 ie 1 122 1 12 11 13 1 K13 1 K13 1 K14 1 K14 1 K14 1 15 1 K15 1K15 1 k16 1 16 Ml cio 1 10 1 K19 1 K19 1 K20 1 K20 1 K21 1 K21 1 K22 1 K22 1 K22 MN kis iiy e SS O SS E E Y MT LZ HI Cancel Each cell in the grid represents a spot on the slide The arrays on the slide are separated by rows and columns in dark color In the demonstration above the spots are arranged in a 20 x CapitalBio Corporation 50 PersonalArrayer 16 Chapter 5 Slide Spotting 20 array and cell X1 Y 1 to cell X20 Y20 constitutes the first array The Tracking Identifier of each spot is shown in the cell For example 1 A1 S1 QC refers to the sample in Al well of plate no 1 with sample ID of S1 and sample name of QC Thus the cells sharing the same Tracking Identifier refer to spot replicates of the same sample on the slide Users can click the Save GAL button to export the sample tracking information into a GAL file as in
5. 11 LAA R ES a e A A A E aed aren 11 AH Ware TASA in 11 LABIOS MUS E E E 11 CapitalBio Corporation I PersonalArrayer 16 LA2 Descriphon and Components ancore aen e eon here ede eee 12 a 12 A a A DPx II ed ET ETE A eae eae 13 O A A E EEEE 13 PEO Back Doa TTT 14 ko Hardware AS A A 14 OIinstatlation Caso lisas 15 A etna tutus tetec soe ed a E nearohe tae teehee TEA 15 1 8 Switch between Spotting and Dispensing Mode sss sese 16 1 9 Swatch berveem Slide and P late Mode T 17 110 Layout e 18 Chapter 2 Solwate Instalacion bicis 19 e 19 22 MS talla tom Requiem id iicidoss 19 e ar OF VG erie TnS a OO PRA Oo Po E A A 19 A e eee ne eae see 19 2S A 22 Chapter 3 SOmware Lt asi 23 De ADV SUN A cd sateiene assualt E roosts tots dupaio lass Meade 23 32 ICUS SLATS ras 23 3 2 1 Launch the System 23 A 24 IA BOSTON CAMION cin 24 A yeaa T 24 ALO VI A 24 SERU ea Se ee PS 25 3 8 Protocol Backup E REStOle tada 25 FIEIS yS M aea e S ai aced han uu ned iebas sat ne ceded cacuuinnl 26 Chapter 4 ON MOU E 27 c ATT 27 42 NETTE All ee 21 4 21 Rimse POstioniC a Dro a E E 29 4 2 2 Dry Position Calibration ooo 30 42 3 SOMICate POSITION Callbra rita ici dU 30 Az REI Ne ETT Dra data 31 42 5 Suda Position eee adds da 32 CapitalBio Corporation II PersonalArrayer 16 4 2 6 Tareet Plate Position ee es 32 42 Sample Plate Position C aibri onenean A A A 33 42 8 Pre dispensime Position D eT TTT 34 4 2 9 Pre spotting Slide Positi
6. 2 Confirm initial position of the Robotic Arm The initial position will be in the upper left extreme after the instrument is power on that is 0 0 0 in the Current Pos Parameters section Please check if the Robotic Arm is actually at 0 0 0 If it is not click the X Home or Y Home or Z Home button to move along the corresponding axis Step 3 Move to the proper position In the Jogging section set the step to the appropriate value and click the buttons to move the Spotting Module or the Dispensing Module directly over the bath and submerge the Pins or the Nozzle under the liquid surface at the proper depth to ensure sonicate or uptake performance Step 4 Save the calibrated position Specify that the X Y Z coordinates will be saved in the check boxes within the Current Pos Parameters section Click the Save button and then confirm to use the current position as the new calibrated position The Spotting Module or the Dispensing Module will move up to the home position along the Z axis 4 2 4 Exhaust Position calibration The Exhaust Position is where the Rinse Basin outlet is located and is used during Dispensing mode It is necessary to calibrate the Exhaust Position to ensure that the Nozzle can hover just above the outlet of basin Please refer to 1 10 to see the location of the basin in the instrument The procedure is the following Step 1 Select Exhaust Select the Exhaust option in the Positions section The X Y
7. Calibrated Pos Parameters section and the current X Y Z coordinates of the Spotting Module or the Dispensing Module will be shown in the Current Pos Parameters section Step 2 Confirm initial position of the Robotic Arm The initial position will be in the upper left extreme after the instrument is power on that is 0 0 0 in the Current Pos Parameters section Please check if the Robotic Arm is actually at 0 0 0 If it 1s not click the X Home or Y Home or Z Home button to move along the corresponding axis Step 3 Move to the proper position In the Jogging section set the step to the appropriate value for example 5 10 mm when the the tip of the Pins or the Nozzle is away from the target position and 1 2 mm when it moves more closer and click the buttons to move the Spotting Module or the Dispensing Module directly over the basin inlet and submerge the Pins or Nozzle below the liquid surface within the inlet of basin at the proper depth PersonalArrayer 16 Chapter 4 Configuration Step 4 Save the calibrated position Specify the X Y Z coordinates to be saved in the check boxes within the Current Pos Parameters section Click the Save button and then confirm to use the new current position as the new calibrated position The Spotting Module or the Dispensing Module will then move up to the home position along the Z axis Warning When moving the axes always be aware of the position of the Pins Disp
8. Center to center spot distance within an array in um between two consecutive Spot a A Distance depositions by the Dispenser It is usually 800um 1500um dependent upon the diameter of the spot Spots Count The number of depositions by the Dispenser namely the number of spots printed by the same Dispenser within an array It 19 not supposed to be greater peee nanie than Max Spot Count Max Spot The maximum number of spots is mainly dependent upon the dimensions of Count the Printable Area and the Spot Distance Refers to how many replicates are required for a single sample It is not Replicate s per Simple supposed to be greater than the product of the values of Spots Count per Channel along X axis and Y axis Array How many blank wells between two neighboring wells which are used for Separation printing Array Refers to how many arrays will be arranged on the plate along each axis It 1s Count not supposed to be greater than the Max Array Count Max Array It is determined by Array Separation First Array Position and how many Count rows columns there are on the plate Anay Indicates whether the arrays share the same sample sequence Replication Pre dispensing Count Pre dispensing Time can be set on this page Please refer to 6 7 for more details CapitalBio Corporation 76 PersonalArrayer 16 Chapter 8 Plate Dispensing 8 8 Sample Sequence Click the Next button on the Array Defin
9. Refer to the Packing List to check for the presence of all components 1 4 Hardware Installation 1 4 1 Before You Start Although PersonalArrayer 16 is intentionally designed to be conveniently set up by non technical end users you have to read the instructions in this manual carefully before you begin the installation process and start using the instrument You should also be completely familiar with the operating procedures and requirements Please follow the installation guidelines completely and correctly to avoid damage to the instrument CapitalBio Corporation 11 PersonalArrayer 16 Chapter 1 Hardware Installation 1 4 2 Description and Components Enclosure Robotic Arm Sensor Power LED Humidifier ee c A Rinse amp Dry Framework qa Slide Deck s Sonicator Sample Plate There are 4 functional units Framework Backboard Enclosure and Platform Important components are the Humidifier vacuum pump peristaltic pump and Sonicator The Framework holds up the instrument The peristaltic pump and vacuum pump are mounted onto the Framework in the rear The multi axis Robotic Arm is assembled on the platform which is the core component of spotting functionality The Enclosure isolates the Platform from ambient environment and human accessibility during running There are interfaces for power pneumatic pressure and liquid conduits on the Backboard 1 4 3 Platform The core of the instrument the P
10. Whether the device is well grounded R Whether the power is shut down During Installation Oo Connect the cables and tubing according to the requirements stated in the user manual and printed marks on the equipment Make sure all the connections are securely plugged in Connect the pneumatic tubing connectors and or adaptors in clean surroundings and make sure there is no pressure leakage in the pneumatic systems O Cover the Nozzle with the Nozzle Mask to avoid airborne dust particles After Installation O Clean the Platform Plate Deck or Slide Deck Enclosure etc with cotton cloth o Clean the Humidifier Sonicator Wash Buffer Bucket and Waste Bucket 1 7 Test Run CapitalBio Corporation Check all cable or wiring connection again Check the Platform and make sure there are no obstacles to obstruct the movements of the pin nozzle Clean the Rinse Basin Wash Buffer Bucket Sonicator and fill them with deionized water Install the application software Power on the instrument launch PersonalArrayer 16 software Check 1f there is any abnormal noise from the motors Conduct functional tests for rinse sonicate dry exhaust and emergency stop respectively 15 PersonalArrayer 16 Chapter 1 Hardware Installation O Carry out Position Calibration then prepare the sample and printing substrates O Run atest routine program to print an array O Refer to Troubleshooting section if there is anything wrong
11. You can decide which slide will be printed first how many slides will be printed and how many slides will be used for Pre spotting The Slide Deck can accommodate up to 16 slides in a 2X 8 arrangement The slides about to be printed should be placed consecutively no gaps ing at i id The Pre spotting slide is required in Spotting Slide Count i the Spotting mode There should be at least Pre spotting Slide Count Po one Pre spotting slide Advanced Slide Option CapitalBio Corporation 43 PersonalArrayer 16 Chapter 5 Advanced Slide Option Pre potting Sidelunit rana Lx 25 000 ox 2 HDD Px 27 000 Min Margin Note 5 Array Definition CapitalBio Corporation 44 Slide Spotting Click the Advanced Slide Option button on the Slide page to show the Advanced Slide Option dialog You can customize the pre spotting slide here by defining the printable area and the Min Margin The printable area of the Pre spotting slide s is the same with other slides Please refer to the illustration of the Spotting Area section Min Margin refers to the minimum space between the border of the printable area and the edge of Pre spotting slide It should not be less than 1 mm OX and OY should not be less than Min Margin PX PY refers to width length of the printable area The maximum is restricted by the slide dimensions and the minimum is related to the Pin Configuration Users will
12. available in this section There are control buttons at the bottom of the page including the Start button Pause button Stop button and the Reprint button Please refer to 9 4 to know more about the Reprint button 5 10 2 Pause and Proceed The pause and the resume functions are provided to handle unexpected emergency events particularly during Spotting applications Click the Pause button to pop up the Pause amp Resume dialog The instrument will enter into halt status after 1t completes the current basic action A basic action refers an action which can not be further subdivided for example the movement of the Robotic Arm along a specific axis CapitalBio Corporation 52 PersonalArrayer 16 Chapter 5 Slide Spotting Pause amp Resume w Continue Wash Re uptake sample L Exit E C Pause after cleaning a Backward Sample Slide T Array Y Array Replicate TA There are several options you can choose after you access the Pause amp Resume dialog Continue Select the actions to execute immediately before the next action in the protocol For example check the Wash box to insert a wash step into the process just before the next action Exit Choose to terminate the current running protocol Check the Home after washing box to bring the Robotic Arm to the home position and carry out a cleaning operation before termination Pause after cleaning Choose to carry out a cleaning o
13. be alerted for an invalid configuration Increasing or decreasing the PX and PY values will increase or decrease Max Spot Count and Max Array Count respectively Click the Next button on the Slide page or click the Array button on the left Task Panel to turn to the Array Definition page Personal A rraver TM 16 Chapter 5 Array Spot Distancetmicrony 200 Spork Count per Pin Max Spot Count 08 353 Replicate per Sample Multi Array Array Separationimmi Array Count Max Array Count Array Replication Pre Spotting Pre Spotting Count Pre spotting Distancet micron Slide Spotting Preview X Direction Y Direction Pa Pai a LC C Y Direction F F La Ts G G i mr GT G 5 ooo eae CO COCOCOOUC COOCOCOCO UC ee 0C ES a E E 0 BackiBi LT N ext gt In this page the user can customize how many Arrays sub arrays will be printed on the slide how many spots will be in an Array and how the Arrays and spots are arranged Users can preview the arrangement on a virtual slide in the box on the right This is the center to center distance in um between two consecutive spots epee printed by the same pin within an Array It is dependent upon the diameter of Distance the spots which are usually 180um 400um The number of deposition actions taken by each pin Specifically the number of Spot Count 7 er Pin spo
14. by the tab Each entry of the sample information should be in a pattern of the Sample ID Sample Name The entry can be blank but you can not skip rows or columns Two neighboring Sample Information Passages are separated by one blank line After editing the sample information entries you can preview the slides to see details of the sample source of each spot as illustrated below Sample Tracking Sample Info Sample Tracking Save GAL Feature Size micron 120 yx xo x10 xt x12 x13 x14 xis x16 x17 x18 x19 x20 Ra x22 yi 1 D6 1 D 1 D 1 D 1 D8 1 D8 1 D8 1 D9 1 D9 1 D9 1 D1O 1 D10 1 D4 1 09 y2 1 D13 11 013 11 014 11 014 1 D14 11 015 1 D15 1 015 1 D16 1 016 1 016 1 017 H 1 610 1 61 Y3 1 020 11 020 1 D20 1 D21 1 D21 1 D21 1 D22 1 D22 1 D22 1 4 1 4 1 64 1 017 1 017 Y4 1E7 1 68 1 68 1 68 19 169 19 1e0 1 10 1 10 LEI 1 11 Ml ies ts Y5 1 E14 1 E14 1 E15 1 15 1 15 1 16 1 16 1 16 1 17 1 17 1 17 1 E18 Miera 1 12 Y6 1 E21 1 E21 IES 1 E22 1 22 1 22 1 4 1 4 1 F4 rs 1 F5 15 Miel 1 18 Y7 ire 1 F9 Fs Fs FO 1 F10 1 F10 1 F11 1 F11 1 6 1 F12 1 12 MB F6 F6 vo lisis 1 F15 1 F16 1 F16 1 F16 1817 1817 1817 1 F18 1 F18 1F18 1 F19 1F12 1 F13 9 1 622 1 F22 122 1 c4 1 64 1 64 1 65 1 65 1 65 l es 1 66 1 G6 1 F19 1 F19 1 69 1 G10 1 G10 1 G10 1 G11 11 611 11 611 11 612 1 612 1 612 1 613 1 G13 Ml c7 1 c7 1 G16 1 G16 1 G17 11 617 1 G17 1 G18 11 618 1 G18 11 619 1 619 1 G19 1 420 MB
15. deionized water Step 3 Click the Rinse button on the Prepare page to wash the fluid lines 10 11 Air Course In Dispensing mode if the instrument is out of use for two days or longer please click the Exhaust button on the Prepare page to expel dust or particles from the Nozzle Please follow the procedure below to switch from the Spotting mode to the Dispensing mode Click the Load Nozzle button on the Prepare page to move the Robotic Arm to Step a convenient position for you to carry out subsequent operations Romove the cover plate on the Z Axis execution module unplug the control Step 2 circuit plug and disconnect the Nozzle Remove the Nozzle and insert the Nozzle Head into the conduit which is connected to the micro valve in the Nozzle to keep the Nozzle from dust Click Exhaust button on the Prepare page and the compressed air will flush the Step 3 air course to expel any contaminants After about 1 minute click the button again to stop Pull the Nozzle Head out of the conduit and then put the Nozzle back into Nozzle Holder Connect the air course and the control circuit plug Step 5 Repeat step 3 Step 4 CapitalBio Corporation 85 PersonalArrayer 16 Chapter 11 Troubleshooting Chapter 11 Troubleshooting 11 1 Overview In this chapter potential errors and problems with PersonalArrayer 16 are listed And their remedies are provided If the problem still can not be solved please co
16. idle Dry ON Vacuum pump is working OFF Vacuum pump is off line Peristaltic Pump ON Peristaltic pump is working Rinse Basin is working OFF Peristaltic pump is off line Rinse Basin is idle 1 4 5 Side View The Emergency Stop button in red is placed on the left hand side of the instrument When the EMS button is pressed down to halt the instrument immediately the Error LED will illuminate Meanwhile a dialog box will appear on the computer screen to prompt you to turn off the instrument After responding to the dialog the user can exit from the program If you intend to restart the instrument after you press the EMS button before turning on the instrument and launching the software you must rotate the button as indicated by the arrows on the button to reset the EMS button CapitalBio Corporation 13 PersonalArrayer 16 Chapter 1 Hardware Installation Note After you press the EMS button please turn off the instrument as instructed by the software Please confirm that the EMS button is reset before restarting the instrument 1 4 6 Backboard The interfaces for power pneumatic pressure and liquid conduits are placed on the Backboard ka w Level Input Pressure Output USB Fan Power Power sensors Pump Inlet Pump Inlet Switch Note Do not block the fan vent or insert anything into the vent 1 5 Hardware Installation Hardware should be installed by professionals In order to ensure the correct and effici
17. in case of unexpected injury PersonalArrayer 16 is provided with safety interlock which will halt the system and wait until the Enclosure is closed again Warning If the Enclosure is damaged please do not use the instrument until it has been inspected by a certified technician Power Cord The power cord is packed with the instrument It has heat insulated PVC material which can apply up to AC450V It must not be replaced with electric wiring of different rating or electric shock fire or damage to the spotter may occur CapitalBio Corporation 5 PersonalArrayer 16 Fuse Fan Safety Precaution Warning We suggest that users do not replace the power supply cord provided by the manufacturer If needed contact the technical support team Tor the CapitalBio PersonalArrayer 16 There are 2 fuses of the same rating in PersonalArrayer 16 with specification of 5mm diameter x 20mm length F 2 5 A 250 V Users can replace them with fuses only of the same rating Warning Please make sure that replacement fuses have the above rating or electric shock fire or damage to the spotter may occur The fan in the CapitalBio PersonalArrayer 16 is necessary for ventilation Do not block or cover the fan vent Blockage will cause the temperature to rise and may result in damage to the spotter possibly causing electric shock and or fire Warning Please do not cover the fan vent on the Backboard of the Capit
18. manual to switch between the Spotting Module and the Dispensing Module and the Plate Deck on the Platform please refer to section 1 9 in this manual to switch between the Slide Deck and the Plate Deck 8 3 Start the System Please refer to section 3 2 to start the PersonalArrayer 16 system The software will identify the current working mode and initialize the interface illustrated as below CapitalBio PersonalArrayer 16 96 Fell Plate Dispensir o s CapitalBio PersonalArrayer 16 Work Flow Cleaning Operations ud Rinze UDisp enser Rinse Dry Dispenser Dry sae Load Plate Home Load Dispenser 8 4 Prepare The application software begins with the Prepare page automatically after launch CapitalBio Corporation 73 PersonalArrayer 16 Chapter 8 Plate Dispensing Alternatively you can click the Prepare button on the left Task Panel to go to the Prepare page Users can load plates on the Plate Deck clean the Nozzle and move the Robotic Arm to the home position Warning Please carry out Position Calibration before you proceed 8 4 1 Cleaning Operations During the cleaning operations the following actions are available Rinse Dispenser Rinse Dry Dispenser Dry Exhaust Please refer to section 6 4 1 for more details Users can load a stand alone Cleaning Protocol from existing files to run a procedure consisting of a series of actions Please refer to section 5 9 for deta
19. of Max Spot l Coni the printable area and the Spot Distance Max Spot Count is determined by the Spot Distance and the PX PY Refers to how many replicates are required for a single sample It should not be Replicate s greater than the product of the values of the Spots Count per Channel along per Sample the X axis and the Y axis Array The distance between the edges of two neighboring arrays It should not be less Separation than the Spot Distance Array Refers to how many arrays will be arranged on the slide along each axis It Count must not be greater than the Max Array Count Max Array Itis determined by Array Separation the size of the array and the printable Count area A a Indicates whether the arrays share the same sample sequence Replication Pre l N j Spot count per sample for Pre dispensing ranging from 0 500 Pre dispensing n i l l Count dispensing is necessary to ensure the uniformity of spots on the slide Pre l E l E s r j The duration of the dispensing during the Pre dispensing step will affect the dispensing Wp l Time volume delivered The unit is us ranging from 10us 2500us CapitalBio Corporation 59 PersonalArrayer 16 Chapter 6 Slide Dispensing 6 8 Sample Sequence a 8 Click the Next button on the array definition page or click the Sample pea button on the left Task Panel to turn to the Sample Sequence page A graphical interface simulating a 384 well plate or a 96 well p
20. the Robotic Arm when the Pin barely makes contact with the slide in the Spotting mode or when the Nozzle tip is 1mm 1 5mm above the surface of the slide in the Dispensing mode Please refer to 1 10 to see the slide location on the instrument Note There should be only one Pin on the Pin Holder while working in Slide Spotting mode The Z coordinate should be recorded independently The procedure is as follows Step 1 Select 1 Slide Select 7 Slide options in the Positions section The X Y Z coordinates that were last calibrated will be shown in the Calibrated Pos Parameters section and the current X Y Z coordinates of the Spotting Module or the Dispensing Module will be shown in the Current Pos Parameters section Step 2 Confirm initial position of the Robotic Arm The initial position will be in the upper left extreme after the instrument is power on that is 0 0 0 in the Current Pos Parameters section Please check if the Robotic Arm is actually at 0 0 0 If it 1s not click the X Home or Y Home or Z Home button to move along the corresponding axis Step 3 Move to the proper position along the X Y axis and save CAUTION In the Jogging section set the step to the appropriate value for the X Y axis and click the buttons to move the Spotting Module or the Dispensing Module directly over the upper left corner of the first slide Specify that the X Y coordinates but not the Z coordinate will be saved in th
21. 2 8 Pre dispensing Position Calibration The Pre dispensing Position Calibration applies to the Dispensing mode It refers to the Z coordinate of the Dispensing Module when you carry out Pre dispensing after sample uptake ensures that the distance from the nozzle to the plate top surface is about 2mm The Nozzle is just above the sample well when Pre dispensing thus only the Z coordinate is involved in the setting of the Pre dispensing Position Calibration Please refer to 1 10 to see the plate location on the instrument The procedure is as following Step 1 Select Pre dispense Select Pre dispense option in the Positions section The last calibrated Z coordinates will be shown in the Calibrated Pos Parameters section and the current Z coordinates of the Dispensing Module will be shown in the Current Pos Parameters section If the position has never been calibrated before the default value will be 0 Step 2 Confirm initial position of the Robotic Arm The initial position on the Z axis will be 0 Please check if the Robotic Arm is actually at x y 0 If it is not click the Z Home button to move along the Z axis It is recommended that you calibrate the Pre dispensing position immediately after the Sample Plate position without moving the Dispensing Module along the X axis and Y axis to ensure the Nozzle is above the plate If it is not above the plate you can choose the Sample Plate Position Calibration and move it to a calibrated po
22. 87 Ay DEING ON ada 75 A or O a TI E ge Gi ere ba ulin 8 AA ele eae tere ee on era me ae mene err ete TI A E TO A 71 LN Run Page Ia yOu eaan E a as 71 s10 2 AAA aa e r e A 78 E A A EEES 78 Chapter 9 Additional Software Features sss sese eee eee 79 e E AA E 79 D2 SEM CHECK TTT 79 9 User Manageme diia oa 79 OD LAdA USET ieee NE A E A E E TE A O EE 80 9 32 Delete USE SA A E EEE AA 81 PEREO a PO E O 81 A A E E E E 81 04 2 E Contigure REDNIH COPs e te tn dieta le 81 DASS REP A snc Mata wmatlanicisnemcnsies 81 Chapter 10 Routine Maintenance sussie ara E 83 IOI Pre Rum and Post Rua les ia 83 IA E 83 IRE Te Lc RAE CR Pe UE EE e Ce een ne ee ee ee ree ee 83 IE a A TTT 83 1 ee N 21 A ner ee ee ete O on PIN err sent Eee a en Or eae Tere teen Stee ener 84 OO INC DICMISM DUCK Cl TTT 84 ORENSE T 84 10 3 Replace Pressure Supply aiii 84 CapitalBio Corporation N PersonalArrayer 16 LOD SOMIC DT E E E A E EN E A A E E E EEA TE TET 84 TOTOE Or LO POE Tm a esosae neta sacee Seacueeesemanicerasaet 85 MOM AT CO 85 Chapter Ll TroublesnOOun asada 87 UO CY E Wie haste ete set oa cee sate taco tel aeut ion ice dae sate st aon tel ncet oc Riu cudub atest alan telaucet ances 87 LEZ PLO DIEM AMC SOLUL OM ei iiaocds 87 CapitalBio Corporation VI Personal A rraver TM 16 Prologue Prologue Thank you for choosing CapitalBio s PersonalArrayer 16 The manual provides all of the necessary information required to carry out applications on th
23. Arrayer 16 Software System hereinafter referred to as System This Agreement is an indispensable part of the System documents You have the right to require the whole documents from the seller of this System in order to protect your rights and interests This System consists of computer software including relevant media printed materials and electronic documents This System may also include any updated or upgraded software and supplemental materials which are provided by CapitalBio for the use of the original System This System and relevant documents shall be granted to you in accordance with this Agreement By installing copying downloading or using this System in any way you agree to be bound by the terms of this Agreement If you do not agree to be bound by the terms of this Agreement Do not install or use this System and return it to the place where you bought it and request a refund of your payment License Grant Subject to the terms of this Agreement CapitalBio hereby grants you a limited right to use this System As a condition of your use of this System you must guarantee that you will not use copy modify rent or assign this System or any portion of it outside the scope of this Agreement CapitalBio Corporation PersonalArrayer 16 Reserved Rights All rights that have not been explicitly authorized to you are reserved by CapitalBio GRANT OF LICENSE CapitalBio grants you the following rights 1 In
24. Corporation 55 PersonalArrayer 16 Chapter 6 Slide Dispensing Alternatively you can click the Prepare button on the left Task Panel to go to the Prepare page Users can load slides on the Slide Deck clean the nozzle and move the Robotic Arm to the home position Warning Please carry out Position Calibration before you proceed 6 4 1 Cleaning Operations The following cleaning operations Rinse Dispenser Rinse Dry Dispenser Dry Exhaust are available for use Idle Dry Dispenser Dry Se Idle Rinse Dispenser Rinse gt A Idle Exhaust Users can always execute these commands independently 6 4 1 1 Rinse Click the Rinse button and the water in the Rinse Basin will begin to M Rinse flow Meanwhile the Rinse Indicator will be illuminated O Rinse Click the Rinse button again to exit current action The Rinse Indicator will turn off Please ensure that there is sufficient water in the Rinse Basin for the following steps CapitalBio Corporation 56 PersonalArrayer 16 Chapter 6 6 4 1 2 Dispenser Rinse 92 Dispenser Rinse Slide Dispensing Click the Dispenser Rinse button the water in the Rinse Basin will begin to flow and the Robotic Arm will move to dip the Nozzle into the basin Meanwhile the Rinse Indicator will be illuminated Dispenser Rinse 6 4 1 3 Dry dd Dry Click the Dispenser Rinse button again to exit the current action The Robotic Ar
25. Define a range of slides plates for reprinting by specifying the one to start with Slide Plate anid iene tiend ok Y direction Array position along X Y axis with specification of the index to start with and X direction the one to end at Only available when there are array replicates Define a range of spot replicates for reprinting by specifying the one to start Replicates P with and the one to end at 9 4 3 Step 3 Reprint Click the Start button on the dialog to start the Reprinting The Reprinting task is carried out just like a normal printing task CapitalBio Corporation 81 PersonalArrayer 16 Chapter 10 Routine Maintenance Chapter 10 Routine Maintenance 10 1 Pre Run and Post Run Cleaning The stand alone Cleaning Protocol should be applied before and after a printing job 10 2 Pins Turn to the Prepare page click the Load Pin button and the Robotic Arm will move to the proper position for the following operation then you can load or replace Pins on the Pin Holder Please keep the following in mind when you load or replace pins O Wear a pair of gloves to avoid the cross contamination Oo Do not touch the shaft and point end of the pin in order to protect the Pin and avoid contamination 6 Do not strike of contact the point end of the Pin with the Pin Holder or it will be damaged How to load Pins Open the Enclosure with care Hold the head end of the Pin with your preferred hand and carefully dire
26. EEN ENER EN 57 6 5 Dispenser CON oura OM sitiar miii 58 ee eT TTT 0 AAA e T E O 58 DA DENO I eck hse Nae acne dida 58 O28 ST eU TT 60 6 8 1 Step 1 Specify Sample Wells on the Virtual Pate aag aata Rava EO aR Rana NOYER avy N 60 PIS 2 Plate SCU HCE AAA Detonator eticloctienoltmode ietemoieied a ee 60 6 8 3 Step 3 Edit the Sample Sequence List ee 60 OSA Stent Advanced OPUOAS eddie 60 08 Slepo Slide T 6l CAC le amie POO CO oranie n T T A a 6l CT TI Nana a E A a eine eeieeeattatsor tee 62 CIO Rum Pace Tay OU ea dis dida 62 610 2 Pause and Proceed id A A RA 62 SUSO DS Geaelsle habla O O tania hie twee aehiiatauecces 62 Chapter 7 Plate PON idol 65 A A O et ae 65 2 Hardware Con RE Te codi E E da lie nuls ireli iodo 65 A An e E T ind as 65 t RT TTT 63 MO an AA O O O eed AO Re ae te modes 66 TAZ Poad PIES a AAA IS 66 PE 0 10 omen ee en em E EC ee eer ee eee ree eres 66 FE OAC PR E E aueanemanrin 66 PICO dd 67 TO Plate CON UN ii 67 AE E A A eae 68 Sample eT a da ed 70 Pad Role atte PROLOG OL 1 sas 70 A E E E N E T E TR EAO 70 AA EST 70 TIO Z Pause and Proceed ada il 71 MA cee eee Ana aan cane eae Ae tee AO nda eee 71 CapitalBio Corporation IV PersonalArrayer 16 Chapter s Plate R L TT ds 73 Ok Rea a 73 9 2 Hardware CON a O 73 Ao E AEA E O eee 73 E eE S N ee ee ea eee 73 BAC AE A T A R 74 L E N EEE E A AA E N E A E A E N E E teks E NA AE A TET 74 O e A 74 So Dispenser COMM UN cis 74 50 late ONEA ON i 74
27. I i 3 Al Sonicator SIT Bath Vacuum Slot Y Axis Rinse Basin A rece i Rinse Basin S Inlet G Sensor 1st Slide Sample Plate Dispensing Module Spotting Module In Slide Spotting or Slide Dispensing Mode Wash Buffer Bucket Input Pump il a L i Er p SI l H Sonicator NT Bath Rinse Basin Outlet c Rinse Basin ae S pi pte outa Inlet OO OOO GO aaa Sensor 1st Plate Sample Plate Dispensing Module ist Pre spotting Slide Spotting Module In Plate Spotting or Plate Dispensing Mode 18 PersonalArrayer 16 Chapter 2 Software Installation Chapter 2 Software Installation 2 1 Overview Only PersonalArrayer 16 application software should be installed onto the computer to connect and control the instrument It is recommended that a person familiar with Microsoft Windows 2000 XP install the software 2 2 Installation Requirements Microsoft Windows XP including Service Pack 2 1s recommended Please refer to 1 2 5 for computer configuration requirements 2 3 Prepare to Install Step Power on the computer Log on as administrator Step 2 Insert the installation CD with PersonalArrayer 16 label into the CD ROM Step 3 Browse the CD find PersonalArrayer 16 Setup exe file and double click 1t to show the installation wizard 2 4 Setup Wizard Fr Select Setup Language Step Choose language pack during setup and click O
28. In Full Sample mode only the sample is taken into the Dispenser channel so the sample uptake can be returned into the sample plate In Partial Sample mode System Liquid such as deionized water is first taken into the Dispenser channel then some air and then the actual sample is taken Here the sample uptake cannot be returned into the sample plate Aspiration Mode CapitalBio Corporation 60 PersonalArrayer 16 Chapter 6 Slide Dispensing It is necessary to customize the number of times that the vacuum drying of the Nozzle is repeated to remove all liquid from the Dr Times after sa d outer surface after aspiration Each vacuum operation lasts for 1 Aspirati Spo second The repeat number is dependent upon the viscosity of the sample Partial Sample Mode Full Sample Mode System Fluid The respective advantages and disadvantages of the two modes are listed in the table below Mode Full sample Partial sample Uptake sequence Sample only System liquid Air Sample Sample uptake gt 35uL gt 5uL Sample reutilization Yes No Maximum spots per uptake gt 5000 gt 200 6 8 5 Step 5 Slide Preview Please refer to section 5 8 6 9 Cleaning Protocol Click the Next button on the Sample Sequence page or click E Clean the Clean button on the left Task Panel to turn to Cleaning Protocol page The Cleaning Protocol can consist of three kinds of operations Rinse Exhaust and Dry A typical C
29. In the Jogging section set the step for Z axis to an appropriate value and click the buttons to move the Spotting Module to make the pin barely make contact with the bottom of the well or move the Dispensing Module to make the nozzle is 1 1 5mm above from the bottom of well Specify that the Z coordinate will be saved in the check boxes within the Current Pos Parameters section Click the Save button and confirm to use the current position as a new calibrated value The Spotting Module or the Dispensing Module will move up to the home position along the Z axis 4 2 7 Sample Plate Position Calibration The Sample Plate setting should use a 384 well plate in the Spotting mode while it may use a 96 well plate or a 384 well plate in the Dispensing mode The Sample Plate Position Calibration depends on the plate type For the 384 well plate the position of the A24 well should be calibrated for the 96 well plate the counter part is the A12 well Please refer to 1 10 to see the plate location on the instrument Note When you are calibrating the Sample Plate position there should be only one Pin on the Pin Holder and the distance between the bottom of the well on the plate and the Pin or Nozzle should be a minimum of Imm The procedure is the following CapitalBio Corporation 33 PersonalArrayer 16 Chapter 4 Configuration Step 1 Select the Sample Plate Select the A24 Well Sample option in the Positions section In the Disp
30. K button Welcome to the PersonalArrayer16 1 0 Setup Wizard This will install Personal rrayerl6 1 0 on your computer It is recommended that you close all other applications before continuing Step 2 Click Nest to continue or Cancel to exit Setup St a rt S creen Cl i ck th e N ex t butt on to proceed CapitalBio Corporation 19 PersonalArrayer 16 Chapter 2 Software Installation fe Setup PersonalArrayer16 1 0 License Agreement Please read the following important information before continuing Please read the following License Agreement You must accept the terms of this agreement before continuing with the installation Step 3 End user agreement Please read it IMPORTANT PLEASE READ CAREFULLY through before you select I This End User License Agreement hereinafter referred to as accept and click the Next button to Agreement is a valid and binding agreement between CapitalBio Corporation hereinafter referred to as CapitalBio and you either an individual or a single entity for the use of Personal arrayer 16 proceed End User License Agreement 5 accept the agreement O I do not accept the agreement fe Setup PersonalArrayer16 1 0 Information Please read the following important information before continuing When you are ready to continue with Setup click Next System Requirements CPU P4 2 06 or higher Step 4 RAM 512M or more S Virtual Memory 512M or more System conf
31. Options Sample Tracking lt Back B Next N gt A graphical interface simulating a 384 well plate is presented to aid the setup of the Sample Sequence for the uptake of sample The procedure is described below 5 8 1 Specify Sample Wells on the Virtual Plate The software provides a set of tools that allow you to specify the sample wells on the virtual plate Click the Single Selection button to select sample well one by one After you select one sample well an automatically incremental ordinal number will be assigned to the well which will be displayed on the center Click the Row Column Selection button to select sample wells row by row or column by column without changing the assigned ordinal numbers of previously selected wells If the Row Column is set to Row gt Col the sample wells will be selected row by row Otherwise they will be selected column by column You can find the Row Column options on the Uptaking Sample dialog page in the Advanced Sample Option dialog box by clicking the Advanced Option button at the bottom of the Sample Sequence dialog page Click the Rectangle Selection button drag a rectangle on the virtual plate to select a block of sample wells within the border of the rectangle without changing any assigned ordinal numbers of previously selected wells inside it The numbering rule will be illustrated later Click the Clear Out button and then click or drag on the virtual plate to 3 dese
32. PersonalArrayer 16 Microarray Spotter User Manual Version 1 0 na ipee s D om da vs CapitalBlo Xa RG A he eqn Gite L a KX Dorporation Copyright Notice 2006 2008 CapitalBio Corporation All rights reserved No part of this publication may be reproduced transcribed transmitted or translated into any language in any form and by any means without the written permission of CapitalBio Corporation Important notice CapitalBio believes that the information in this document is accurate The document has been carefully reviewed for technical accuracy In the event that technical or typographical errors exist CapitalBio reserves the right to make changes to subsequent editions of this document without prior notice to holders of the edition The reader should consult CapitalBio if errors are suspected INNO EVENT SHALL CAPITALBIO BE LIABLE FOR ANY DAMAGE ARISING OUT OF OR RELATED TO THIS DOCUMENT OR THE INFORMATION CONTAINED IN IT TRADEMARKS CapitalBio PersonalArrayer 16 is a registered trademark of CapitalBio All rights reserved CapitalBio PersonalArrayer 16 Software End User License Agreement IMPORTANT PLEASE READ CAREFULLY This End User License Agreement hereinafter referred to as Agreement is a valid and binding agreement between CapitalBio Corporation hereinafter referred to as CapitalBio and you either an individual or a single entity for the use of the Personal
33. Position Calibration should also be carried out after any instrumentation changes or maintenance to ensure that the precise location is determined and to avoid any potential problems The Position Calibration page of the System Configuration dialog consists of 4 sections Positions Calibrated Pos Parameters Current Pos Parameters and Jogging The Position Calibration page in the Slide Spotting mode is as following Warning Please press the Z Home button to lift the Pin or Nozzle up along the Z axis before the Position Calibration occurs in order to eliminate the possibility of collision CapitalBio Corporation 27 PersonalArrayer 16 Chapter 4 SLIEN 1 URT UT ative Position Calibration sc Options of Positions Y Rinse L Dry C Sonicate C ist Slide C A24 Well Sample Ly Peristaltic Calibrated Pos Parameters mm v 320 015 Y 76 022 7 20 980 Current Pos Parameters mm MV x 265 100 M Y 57 988 e z 0 000 Save Jogging mm X Step 2 X Left X Right Xto Calibrated Pos Y Step 0 Y Forward ly Backward Y to Calibrated Pos ganm Up Z Down Z to Calibrated Pos X Home Y Home Z Home Open Backup Cancel Configuration Depending on your selection in the Positions section the coordinates will be loaded and shown in Calibrated Pos Parameters section The following part of this manual describes the operation for the calibration of posistions for rinse dry sonica
34. The user can choose to resume to exit the program to pause after clean or to go back Or the user can click the Stop button to exit the program immediately The program can go back to a previous position to Reprint missing spots Please refer to section 9 4 for details 3 8 Protocol Backup amp Restore e CapitalBio Corporation Click the Save Protocol button to save the protocol as an Array Protocol File with sap suffix 25 PersonalArrayer 16 Chapter 3 Software Tutorial K Click the Open Protocol button to deploy a protocol from an Array Protocol File with sap suffix and confirm After you successfully save the current protocol or load an existing one you can double click the P button on the status bar at the right bottom corner of the window to bring out a dialog to check the path name of the current protocol Note It is recommended that you save the protocol before running A 3 9 Exit System Step 1 Exit the running program or wait until it is completed Step 2 Exit the application software Step 3 Power off the instrument CapitalBio Corporation 26 PersonalArrayer 16 Chapter 4 Configuration Chapter 4 Configuration 4 1 Overview The system configuration options and guidelines are provided in this chapter After the installation of the PersonalArrayer 16 application software the user should check the system configuration including Position Calibration parameters velo
35. Z coordinates that were last calibrated will be shown in the Calibrated Pos Parameters section and the current X Y Z coordinates of the Dispensing Module will be shown in the Current Pos Parameters section Step 2 Confirm initial position of the Robotic Arm The initial position will be in the upper left extreme after the instrument is power on that is 0 0 0 in the Current Pos Parameters section Please check if the Robotic Arm is actually at 0 0 0 If it is not click the X Home or Y Home or Z Home button to move along the corresponding axis Step 3 Move to the proper position In the Jogging section set the step to the appropriate value and click the buttons to move the Dispensing Module directly over the basin outlet and aim the Nozzle toward the centre of the basin outlet Step 4 Save the calibrated position Specify that the X Y coordinates will be saved in the check boxes within the Current Pos Parameters section Click the Save button and then confirm to use the current position as the new calibrated position and the new coordinates will be shown in the Calibrated Pos Parameters CapitalBio Corporation 31 PersonalArrayer 16 Chapter 4 Configuration 4 2 5 Slide Position Calibration In the Slide Spotting or the Slide Dispensing mode it is necessary to calibrate the 1 Slide Position The X and Y coordinates represent the upper left corner of the slide and the Z coordinate represents the position of
36. alBio PersonalArrayer 16 Otherwise the temperature will rise and result in damage to the spotter possibly causing electric shock and or fire Moving Parts Water Moving parts in the interior of the instrument may also cause physical injury Under normal operation the Enclosure protects the user from such hazards Warning Do NOT attempt to access the interior of the instrument while it is running The CapitalBio PersonalArrayer 16 has some components such as the Sonicator Bath Humidifier and the Wash Buffer Bucket which must be filled with some water for daily operations The Humidifier should be filled with deionized water The Wash Buffer Bucket should be filled with deionized water or other buffer The Sonicator Bath should be filled with deionized water or other buffer All water or buffers should be replaced daily There are two syringes in the accessory pack Always use one of them to fill the Sonicator Bath and use the other to take the fluid out of the Sonicator Bath Sample Requirements Fabrication of nucleic acid or protein microarrays may be undertaken on the CapitalBio PersonalArrayer 16 with either the contact Spotting Module or the non CapitalBio Corporation 6 PersonalArrayer 16 Safety Precaution contact Dispensing Module The properties of the sample are an important factor influencing the production of the microarray and the quality of microarray chips To fulfill the quality specifica
37. ame and password on the login dialog The software will detect the instrument identify the working mode and launch self test PersonalArrayer 16 can switch between four working modes as Slide Spotting Slide Dispensing Plate Spotting and Plate Dispensing for 96 well plate The software will identify which is the current working mode according to hardware configuration of the instrument and initialize the corresponding interfaces Note If the self test failed please restart the instrument and software as following o Power off the instrument O Exit the software O Restart the instrument and software According to user s interests and familiarity with the system the software provides two experience styles for running Guided Style New users and those who are not familiar enough with the system can choose the Guided Style to run a printing program step by step by clicking Next button to proceed Expert Style Experienced users can click the buttons on the left Task Panel to access any particular page directly with more flexibility The two styles are both integrated into the user Users can employ both styles at will and at the same time the software provides guided control of new steps until the user is familiar with the process CapitalBio Corporation 23 PersonalArrayer 16 Chapter 3 Software Tutorial 3 3 Configuration It is mandatory to reset the configuration parameters particularly to perform Pos
38. an click the Save button to backup the current protocol or click the Open button to load an existing protocol 5 10 Run Click the Next button on the cleaning protocol page or click the Run button on the left Task Panel to turn to the run page Click the Start button to run the protocol CapitalBio Corporation 51 PersonalArrayer 16 Chapter 5 Slide Spotting 5 10 1 Run Page Layout Slide Info Sample Plate 1 A q A L a DIO Slide 3 Pre Spotting H Time Elapsed 0 Day 00 Hour 01 Minute 49 Second X Array 1 Array 1 Time Left 0 Day P Pat Replicate Reminder Preprin lt Back B The Slide Info section reveals the current status of the slides including the current sample current slide and if the Array Replication is true the row index and the column index of the current array and the index of current replicate The Plate section illustrates the status of the current sample plate including the plate index which wells have already been sampled which ones are being sampled right now and which ones have not yet been sampled The wells at different status levels are differentiated by different colors The Progress section describes the progress on various levels with bars including the Pre spotting progress Spotting progress and plate progress The time statistics and estimation an information section is also
39. aracteristics of the sample Click the Set to Default button to load the default settings 4 4 Miscellaneous Users can choose whether to apply humidity control and use the plate chiller The specification of target relative humidity in percentages 1s described on this page If you want to apply humidity control please confirm that there is enough water in the humidifier before you run the experiment System Configuration Position Calibration Misc W Control Humidity Target Humidity 45 Plate Chiller In the check boxes Select either plate chiller or humidity control If humidity control is chosen enter a relative humidity value in the Target Humidity box 4 5 Backup and Restore Confirm that all necessary modifications are put on the System Configuration dialog box and click the OK button at the bottom of the dialog box to apply the modifications save them into the System Configuration file and then exit the dialog box You can click the Backup button to save the data as a System Configuration file sas Click the Open button and confirm when notified to restore the settings previously saved by selecting a sas file CapitalBio Corporation 37 PersonalArrayer 16 Slide Spotting Chapter 5 Slide Spotting 5 1 Overview The work flow and instructions for microarray spotting onto slides with the PersonalArrayer 16 are described in this chapter After reading the chapter through the user will have gain
40. ase contact CapitalBio Address CapitalBio Corporation 18 Life Science Parkway Changping District Beijing 102206 P R China Tel 86 10 80725793 Fax 86 10 80726782 Website http www capitalbio com Email techsupport capitalbio com globalsales capitalbio com CapitalBio Corporation II PersonalArrayer 16 Index Prol US ner iaa Manual Cont T TT Technmolosy S W ORIG ea lada l TECOS A AA da l Wy Orie a L 2 NOES Renee ate er ee ae eae a Orne tent en E ene RE RES E ene eran eee 2 Sis ee ere gent nor CS me oe Ra Oe ee 3 DAILY PRECAUTION T 5 Certification Identification and Power Supply Label sss sese 5 TOE OS is noe eS 5 PO VS O EH 5 PSS H aE e E E eE des aa hace ea a E 6 A E ee OR Re E ee eR ee eee ees 6 Movino PAINS iii 6 A A oes at te wade O oat ot alu aa da ates 6 SES 0 1 001 0 be een eo ene re a ne 6 SSC E TT 7 Emergency Stop DUO asia E SOIG A o e o 5 7 Chapter Hardware Installation 9 DOV CIVIC W O Oa E a a beisineeeades tees 9 l Tnstallaton Requires ments da 9 Re A II O O a 9 12 2 A TTT 9 s TOWN OT 9 1 2 4 Electromagnetic Compatibility EMO occccccccccccnnonenennnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncnnnnnnnnnnnnnnnnos 9 1 25 Computer Workstation a a rola els 10 1246 Press re Suppi regure menis A A a 10 IR Receiving INSPECTION aiii etana dan goed Male easmaa R cna teak 11 1 3 1 Initial Inspection upon Receipt Of Equipment sss esse eee eee eee eee 11 A A ede A EE nade A E nade E A EE
41. city and acceleration Dispense options will be available in the Dispensing mode The system configuration parameters are crucial to the performance of the instrument Improper configuration could lead to damage It 19 recommended that only a person familiar with the system can modify the settings O Click the Configuration button on the tool bar in the upper right corner of 7 the main frame to access the System Configuration dialog You can modify and reset the following parameters Rinse position calibration please refer to section 4 2 1 Dry position calibration please refer to section 4 2 2 Sonicate System Liquid position calibration please refer to section 4 2 3 Position Exhaust position calibration please refer to section 4 2 4 Calibration Slide position calibration please refer to section 4 2 5 Target plate well position calibration please refer to section 4 2 6 Sample plate well position calibration please refer to section 4 2 7 Pre dispense position calibration please refer to section 4 2 8 Pre spotting slide position calibration please refer to section 4 2 9 Dispense Please refer to section 4 3 Setting Miscellaneous Please refer to section 4 4 4 2 Position Calibration Position Calibration refers to determining and recording the locations of several components on the microarray spotter which are critical to different steps during Spotting or Dispensing operations
42. ct the point end of the pin to the hole on the Pin Holder and insert it into the holder Then take the head end of the Pin with tweezers to lift 1t carefully and avoid deflection or shaking as much as possible Lower the head end of the Pin into the slot on the Pin Holder and make sure it can be lifted or dropped smoothly through the slot How to unload Pins Open the Enclosure with care Hold the head end of the Pin with your preferred hand carefully lift 1t slightly while avoid deflection or shaking as much as possible Then hold the head end of the Pin with your other hand and lift it vertically out the holder Cover the point end of the Pin with the sheath and put away the Pin back into the box Note If the instrument will be not used for a long period of time please run a stand alone protocol to clean the Pins then unload the Pins and store them safely Lower or raise the pin carefully in straight alignment with the pin hole to avoid bending the pin shaft or contacting the point of the pin with the pin hole 10 3 Nozzle Please run a stand alone Cleaning Protocol after each run then cover the Nozzle with the nozzle enclosure to protect it from contamination and clogging If the instrument will not be used for a long period of time please unload the Nozzle and store it safely in its box 10 4 Slide Deck The Slide Deck provides a flat surface to carry slides Please handle it with care when you mount or dismount it from the instrum
43. de Spotting removing excess liquid Pre spotting The distance in um between spots on Pre spotting slides can range from 80um Distance 4500um J Homogen Array He ge Array E L Spot Distance O ooo Array Separation The figure illustrates that the spots printed by the same Pin constitute a Homogen Array within an Array The number of Homogen Arrays in an Array is always the same with the number of Pins on the Pin Holder In the illustration above there are 4 Pins 2 by 2 configuration on the Pin Holder the Array is 4 by 4 There are 4 Homogen Arrays in an array and the Homogen Array is 2 by 2 The Spotting Module will move up and down for 4 times alternatively 1t will take 4 deposition actions of the Spotting Module to complete an Array Thus the Spot Count per Pin is 2 by 2 X by Y the Array Count is 2 by 4 X by Y 5 8 Sample Sequence BR Click the Next button on the Array Definition page or click the Sample button on the left Task Panel to turn to the Sample Sequence page CapitalBio Corporation 46 PersonalArrayer 16 b ETTET Chapter 5 384 Well Plate Slide Spotting Z 2 v O 24 aa ol r oo is I r r P ee pee 9 999 f f r Taa L 32 s 4 EES ED as ffe Pla 57 Mos Moo 2 Sample Block s Count Selected T Max 121 121 Advanced
44. e in kPa Ratio of Dispense time to Aspiration time A fractional number Aspiration Time Refers to the time applied to take up washing buffer or water in seconds Exhaust time Refers to the time required to exhaust the washing buffer or water in seconds Drying time Refers to the time required for vacuuming after washing in seconds Dispense CapitalBio Corporation Aspiration pressure Refers to the pressure applied to take up the sample or the system liquid preparations in kPa System liquid aspiration time Refers to the time required to take up the system liquid in seconds Air aspiration pressure Refers to the pressure applied to inhale air to separate sample and System Liquid in kPa Air aspiration time Refers to the time required to inhale air in seconds Sample aspiration time Refers to the time required to take up the sample in seconds Dispense pressure Refers to the pressure applied to dispense the sample through the nozzle onto the substrate in kPa Drying time Note Refers to the time required for vacuuming after taking up sample or system liquid in seconds The Dispense pressure should be no less than 3 kPa and the Dispensing Time no less than 250us The Sample aspiration time and Dispense pressure may be modified E 2 PersonalArrayer 16 Chapter 4 Configuration according to the viscosity and surface tension ch
45. e Nozzle onto the Nozzle Holder Restart the application software after you switch the module 1 9 Switch between Slide and Plate Mode Users can conveniently replace the Slide Deck with the Plate Deck or vice versa to switch the instrument between slide and plate mode The procedure 1s as following Step Turn to the Prepare page click the Load Slides or the Load Plates button and the Robotic Arm will move to a proper position for the following operation Step 2 Unscrew the 4 bolts on the corners of the Slide Deck and remove the deck Step 3 Align the Plate Deck to the positioning pin on the Platform and place it with care Step 4 Screw the 4 bolts at the corners Step 5 Exit the program and launch it again Step 6 Check the interface to confirm the program has identified the hardware configuration and initialized the instrument in Plate Spotting or Plate Dispensing mode correctly The procedure to replace the Plate Deck for the Slide Deck is similar Note Please remove all slides or plates from the deck before you switch the decks to avoid potential damage to slides or plates Please restart the application software after you switch the decks CapitalBio Corporation 17 PersonalArrayer 16 Chapter 1 Hardware Installation 1 10 Layout Scheme PersonalArrayer 16 system layout scheme is illustrated below CapitalBio Corporation Waste Bucket Output Pump la E LZ e
46. e check boxes within the Current Pos Parameters section Click the Save button and then confirm to use the current position as the new calibrated position Step 4 Move to the proper position along the Z axis and save CAUTION In the Jogging section set the step to the an appropriate value for the Z axis and click the buttons to move the Spotting Module to make the Pin barely contact with the surface of the slide or move the Dispensing Module to hover it over the slide with 1mm 1 5mm distance Specify the Z coordinate but not the X Y coordinates to be saved in the check boxes within the Current Pos Parameters section Click the Save button and then confirm to use the current position as a new calibrated position The Spotting Module or the Dispensing Module will move up to the home position along the Z axis 4 2 6 Target Plate Position Calibration The PersonalArrayer 16 supports up to two plates and it is necessary to calibrate the H1 well positions of each target plate position respectively Calibration 1s necessary to ensure that the solo Pin or the Nozzle can aim at the center of the H1 well of the plate and that the Pin should barely contact with the bottom of the well in the Spotting mode In the Dispensing mode the Nozzle should be 1 1 5mm above of the bottom of the well in the The Z axis height can be calibrated once for all plates Please refer to section 1 10 to see the plate location on the instrument CapitalBio Cor
47. e instrument Please read it through follow the instructions and observe all the cautions and limitations Before you go on verify that the instrument you are going to operate 19 PersonalArrayer 16 manufactured by CapitalBio Corporation In the prologue general information about PersonalArrayer 16 is provided Abbreviations and alternative names are listed as well Manual Content Chapter Content Safet Provides crucial information to use the system _ safely 7 c All PersonalArrayer 16 users should read this chapter before Precautions E l installing and using the system Hardware Provides Personal Arraver 16 hardware specifications and step by Installation step instructions for installation of the system Software Provides instructions on how to install the PersonalArrayer 16 Installation application software and the device drivers Software Provides brief instructions on basic operations for Spotting and Dispensing and instructions on how to run the system for a test Tutorial i l l immediately after the hardware and software installation Provides instructions on how to configure the system parameters Configuration f E E before Spotting or Dispensing Slide Spotting Provides detailed instructions on Slide Spotting workflow Slide Dispensing Provides detailed instructions on Slide Dispensing workflow Plate Spotting Provides detailed instructions on Plate Spotting workflow Plate D
48. eady been sampled which ones are being sampled and which ones have not yet been sampled The wells at different status levels are differentiated by different colors The Progress section describes the progress on various levels with bars including the Pre dispensing progress Dispensing progress and plate progress The time statistics and estimation and an information section is also available in this section There are control buttons at the bottom of the page including the Start button Pause button Stop button and the Reprint button We will continue to discuss the Pause button and Stop button below Please refer to section 9 4 to learn more about the Reprint button 6 10 2 Pause and Proceed The pause and resume functions are provided to handle unexpected emergency events particularly during Dispensing applications Click the Pause button to bring up the Pause amp Resume dialog The instrument will enter into halt status after it completes the current basic action The basic action refers an action which cannot be subdivided for example movement of the Robotic Arm along a specific axis There are several options available after you access the Pause amp Resume dialog Please refer to section 5 10 2 for more details Click the OK button to execute corresponding operations If the system is halted the Pause button will appear as the Continue button and users can click it to resume the current protocol 6 10 3 Stop You can
49. ed essential skills in Slide Spotting procedures and for instrument and related software operations 5 2 Hardware Configuration In the Slide Spotting mode the Spotting Module should be fitted on the Robotic Arm please refer to section 1 8 in the manual for instructions on changing between the Spotting Module and the Dispensing Module and the Slide Deck should be fitted on the platform please refer to section 1 9 in the manual to switch between the Slide Deck and the Plate Deck 5 3 Start the System Please refer to section 3 2 to start the PersonalArrayer 16 system If the hardware 19 correctly configured as described in section 5 2 the software will identify the current working mode and initialize the interface illustrated as below a CapitalBio PersonalArrayerl6 Slide Spotting Prepari s CapitalBio D PersonalArrayer 16 Work Flow Cleaning Operations Protocol of Cleaning ii Rinse Protocol File Pin Rinze h Load Slide Home Load Pin 5 4 Prepare The application software begins with the Prepare page automatically after launch Alternatively you can click the Prepare button on the left Task Panel to go to the Prepare CapitalBio Corporation 39 PersonalArrayer 16 Chapter 5 Slide Spotting page Users can load the Pin s onto the Pin Holder load slides on the Slide Deck clean the Pin s and move the Robotic Arms to the home position Warning Please carry out Position Calibration before
50. either select the Exit option on the Pause amp Resume dialog or click the Stop button CapitalBio Corporation 62 PersonalArrayer 16 Chapter 6 Slide Dispensing when the system is halted CapitalBio Corporation 63 PersonalArrayer 16 Chapter 7 Plate Spotting Chapter 7 Plate Spotting 7 1 Overview The work flow and instructions for microarray Spotting onto plates with the PersonalArrayer 16 are described in this chapter After reading this chapter the user will have a basic understanding of Plate Spotting procedures and have gained essential skill in instrument and software operations 7 2 Hardware Configuration In the Plate Spotting mode the instrument should be equipped with the Spotting Module on the Robotic Arm please refer to section 1 8 in this manual to switch between the Spotting Module and the Dispensing Module and the Plate Deck on the Platform please refer to section 1 9 in this manual to switch between the Slide Deck and the Plate Deck 7 3 Start the System Please refer to section 3 2 to start the PersonalArrayer 16 system If the hardware is correctly configured as described in section 7 2 the software will identify the current working mode and initialize the interface illustrated as below a Capital io PersonalArrayerl6 96 Fell Plate Spotting _ WE CapitalBio ay PersonalArrayer 16 Cleaning Operations a Rinse l PinRinse w Load Flate Home Load Fir 7 4 Pre
51. enser Make sure that the planned routines of all the moving components are clear of any obstacles before you apply actual movement to avoid potentially disastrous outcomes 4 2 2 Dry Position Calibration The Dry Position is where the Vacuum Slots are located It is necessary to calibrate the Dry Position to ensure that all 4 Pins on the Pin Holder or the Nozzle can descend into the inhalant hole s Please refer to 1 10 to see the location of the Vacuum Slot on the instrument The procedure is as following Step 1 Select the Dry Select the Dry options in the Positions section The X Y Z coordinates that were last calibrated will be shown in the Calibrated Pos Parameters section and the current X Y Z coordinates of the Spotting Module or the Dispensing Module will be shown in the Current Pos Parameters section Step 2 Confirm initial position of the Robotic Arm The initial position will be in the upper left extreme after the instrument is power on that is 0 0 0 in the Current Pos Parameters section Please check if the Robotic Arm is actually at 0 0 0 If it 1s not click the X Home or Y Home or Z Home button to move along the corresponding axis Step 3 Move to the proper position In the Jogging section set the step to the appropriate value and click the buttons to move the Spotting Module or the Dispensing Module directly over the Vacuum Slot and insert the Pins or Nozzle into the inhalant holes at the proper dep
52. ensing mode a combo box will be activated and you can choose to use the 96 well plate or the 384 well plate If you choose the 96 well plate the calibration position label will change into the A12 Well Sample The last calibrated X Y Z coordinates will be shown in the Calibrated Pos Parameters section and the current X Y Z coordinates of the Spotting Module or the Dispensing Module will be shown in the Current Pos Parameters section Step 2 Confirm initial position of the Robotic Arm The initial position will be in the upper left extreme after the instrument is power on that is 0 0 0 in the Current Pos Parameters section Please check if the Robotic Arm is actually at 0 0 0 If it 1s not click the X Home or Y Home or Z Home button to move along the corresponding axis Step 3 Move to the proper position In the Jogging section select the appropriate value and click the buttons to move the Spotting Module or the Dispensing Module directly over the centre of the A12 A24 well and then submerge the Pin or Nozzle into the sample to a depth that is sufficient to ensure reliable sample uptake Step 4 Save the calibrated position Specify that the X Y Z coordinates will be saved in the check boxes within the Current Pos Parameters section Click the Save button and confirm to use the current position as a new calibrated value The Spotting Module or the Dispensing Module will move up to the home position along the Z axis 4
53. ent Before printing job please clean the surface of Slide Deck with cotton cloth and alcohol CapitalBio Corporation 83 PersonalArrayer 16 Chapter 10 Routine Maintenance After finishing a printing job please remove all the slides on the deck If the deck will not be used for a long period of time please put it away in its box for storage 10 5 Plate Deck The Plate Deck provides a flat surface to carry plates Please handle it with care when you mount or dismount it from the instrument Before the printing job please clean the surface of plate deck with cotton cloth and alcohol After the printing job please remove all the plates on the deck If the deck will not be used for a long period of time please put it away in its box for storage 10 6 Replenish Buckets There are 2 water buckets for PersonalArrayer 16 the Wash Buffer Bucket and Waste Bucket Before each printing job please check and ensure that the Wash Buffer Bucket is full and that the Waste Bucket is empty If the program will run for a long period of time please check the status of buckets regularly If the water runs low or the waste level is high the application software will alert you please pause the program replenish the Wash Buffer Bucket and empty the Waste Bucket and then resume 10 7 Replenish Humidifier The Humidifier is used to maintain a constant relative humidity inside the instrument Before each printing job please unplug
54. ent operation of the instrument the user should become familiar with the construction and functionality of the instrument The user should also be awear of the interchange procedure s from Spotting Module to Dispensing Module or from Slide Deck to Plate Deck Step 1 Place the instrument on a stable level work bench Step 2 Take out the tubing Wash Buffer Bucket and Waste Bucket from the package follow the instructions below to connect the input pump output pump and two buckets and then plug the adapters of the bucket level sensors into the corresponding female ends on the Backboard CapitalBio Corporation 14 PersonalArrayer 16 Chapter 1 Hardware Installation Step 3 Please refer to section 1 2 6 to prepare the pressure source and then connect the pressure source to the inlet on the Backboard with the 4mm outer diameter PU tube Step 4 Connect the instrument to the computer with the USB cable Step 5 Connect the instrument to the power net with the power cord The instrument should be grounded via the power cord to avoid electrical shock 1 6 Installation Check List Before Installation Make sure the power input 1s the same as the rated power requirements Refer to 1 2 3 It is recommended to use a UPS of AC 110 V 220 V 750 W Inspect the instrument to check R Whether the connectors and terminals are connected inserted and fastened correctly R Whether there is any liquid spillage or pools R
55. equirements and installation procedures and inspection details configuration switching of Dispensing Module and Spotting Module switching of Slide Deck and Plate Deck and the overall layout of the instrument 1 2 Installation Requirements 1 2 1 Environment The PersonalArrayer 16 should be placed in a clean room that meets the following environmental conditions Spotting or Dispensing environmental requirements Site Requirement Indoor Use Cleanliness degree 10000 class meets or exceeds GMP requirements Temperature Range 5 30 C Relative Humidity Range 30 50 Altitude Up to 2000m Note Because the microarray workstation is a precision instrument please keep the environment as clean as possible Install the microarray workstation away from sunlight ventilation ducts and any other devices that may cause significant change in temperature and humidity 1 2 2 Space Length mm Depth mm Height mm 560 500 435 1 2 3 Power Frequency Hz 50 60 Rated Voltage V AC 100 240 Maximum Input Current A l Rated Power W 250 Fuse 5 0A 125V 1 2 4 Electromagnetic Compatibility EMC A mild EMC environment is desirable for optimal functioning of the instrument Strong CapitalBio Corporation 9 PersonalArrayer 16 Chapter 1 Hardware Installation electromagnetic fields may lead to unpredictable results The following cautions should be considered O Keep the instrument away from devices ir
56. f the Spotting Module to compensate for the difference between the liquid level in the sample well and the calibrated sample plate position The positive compensation moves the Pin s further downward and negative compensation moves the Pin s less downward Delay time for Customize the length of time the pin is in contact with the sample uptake sample dependent upon the nature of the sample Compensation of Z position Max spots count Set the maximum number of spots printed per uptake dependent per uptake upon the nature of the sample CapitalBio Corporation 48 PersonalArrayer 16 Chapter 5 Slide Spotting Delay time for Customize the length of time the Pin remains in contact with the spotting slide dependent upon the nature of the sample The travel distance of the Spotting Module along the Z axis Lifting stroke from the peak when 1t moves upward to the extreme to the calibrated slide position The travel distance of the Spotting Module along the Z axis Dropping stroke from the calibrated slide position to the trough when 1t moves downward to the extreme 5 8 5 Slide Preview Click the Sample Tracking button to preview the distribution of the samples on the slides in the Sample Tracking dialog There are two pages Sample Info page where a virtual 384 well plate is provided to browse and edit sample information and Sample Track page to provide a preview interface You can also annotate t
57. g rinsing and vacuum drying which decreases or eliminates most cross contamination among samples The Humidifier Plate Chiller and HEPA Filter each contribute to the high fabrication quality of the microarrays Working Mode PersonalArrayer 16 can switch between four working modes as listed below Working Mode Substrate Distribution Technology Slide Spotting Slide Contact Spotting Slide Dispensing Slide Non contact Dispensing Plate Spotting Plate Contact Spotting Plate Dispensing Plate Non contact Dispensing Notes The path name you specified for a customizable user file should conform to the naming rules of Windows operating systems without slash backslash comma and other characters that are not compatible with Windows systems etc It is recommended that the instrument software is installed by professionals familiar with Windows 2000 XP Below are abbreviations and the corresponding full terms Instrument PersonalArrayer 16 Microarray Spotter Spotting Module The module consists of Pin s and Pin Holder l l The module consists of a Nozzle a Nozzle Holder control circuits Dispensing Module and air courses Spotting Contact Spotting Dispensing Non contact Dispensing Plate Deck The platform carrying microplates when printing on plate substrates Slide Deck The platform carrying slides when printing on slide substrates HEPA Filter The air filter removes at least 99 97 of airborne particles as small
58. he Robotic Arm to the home position the top left corner of the Platform If any of the cleaning operations is running the home command will stop it CapitalBio Corporation 57 PersonalArrayer 16 Chapter 6 Slide Dispensing 6 5 Dispenser Configuration Wp Click the Next button on the Prepare page or click the Dispenser button on PENSE the left Task Panel to turn to the Dispenser Configuration page PersonalArrayer 16 curently has a single Dispenser Nozzle This combination can not be changed 6 6 Slide Configuration Click the Next button on the Dispenser Configuration page or click Dispenser the Slide button on the left Task Panel to turn to the Slide page This page consists of two sections Dispensing Area and Slides Info Please refer to section 5 6 Spotting Area to know more about parameters in the Dispensing Area section In the Slide Info section users can specify the number and location of the slides You can decide which slide will be printed first and how many slides will be printed In the Slide Dispensing mode the Pre dispensing operation returns excess sample to the sample well on the sample plate so there is no need to set up Pre dispensing slides Advanced Slide Option Click the Advanced Slide Option button on Lx 25 000 E the Slide page to show the Advanced Slide Option dialog You can customize the Min Margin The Min Margin refers to the minimum space between the border of the printable a
59. he plate design Click the Add button to submit and add all the indexed sample wells on the current plate into the Sample Sequence list The selected sample blocks should not exceed the maximum or you will be alerted and the submission will be rejected 5 8 3 Edit the Sample Sequence List The user still can modify sample sequence list entries The following commands are available on the top of the list box Delete Delete All Copy Paste Move Up and Move Down If for some reason you did not already pipette any sample into an indexed sample well in the list you can select the entry and click the Set as Blank button and the instrument will skip that well on the sample plate Click the Set as Sample to restore the blank entry 5 8 4 Advanced Options Click the Advanced Slide Option button to pop up the Advanced Sample Option dialog and configure a set of parameters The parameters are organized into two dialog pages the Spotting Settings dialog page and the Uptaking Sample dialog page Spotting Settings Uptaking Sample Sample Index Priority Spotting Settings Uptaking Sample Row Column S Row gt Col C Col gt Row Row S Left gt Right Right gt Left Delay time 51 0 01 Lifting stroke mmi 2 Compensation of Z position mm 0 Dropping stroke mrm 1 pe po mm Delay Time s 1 Max Spots Count Per Uptake 500 L The Row Column option and the Row option have been explained in section 5 8 1 Adjust the Z axis position o
60. he plate is pressed against the clasp on the Plate Deck 7 4 3 Home Click the Home button to move the Robotic Arm to the home position at the top left corner of the Platform If any of the cleaning operations is running the home command will stop it 7 4 4 Load Pin Click the Load Pin button and the Robotic Arm will move the Spotting Module to the front CapitalBio Corporation 66 PersonalArrayer 16 Chanter 7 Plate Spotting for the convenience of users to load a single pin Warning In Plate Spotting mode there should be only 1 Pin on the Pin Holder at the back right corner Additional pins or Pins in the incorrect position in the Pin Holder may result in malfunction or damage failure and sample contamination etc 7 5 Pin Configuration pi Click the Next button on the Prepare page or click the Pin button on the a left Task Panel to turn to the Pin Configuration page In the Plate Spotting mode there should be only 1 Pin in the Pin Holder Thus the combination is fixed 7 6 Plate Configuration alah Plat Click the Next button on the Pin Configuration page or click the Plate gg button on the left Task Panel to turn to the Plate page Plate Info Plate Layout OOOO O OOOO OOO OOO OOO COLI OOOODOOO OOOOOCOO Users can specify the number and DGG O O location of the plates You can 5 CD COO OO OT decide which plate will be printed first and how many plates will be printed You can also decide ho
61. he samples and export the GAL file You should follow the instructions below Step 1 Select which plate will be edited in the Plate No combo box Step 2 The Sample Info Working Area is a virtual 384 well plate The wells with a grey background will be used in the printing job the ones with a white background will not All the wells can be edited but only the ones with grey background can be associated with the sample sequence Step 3 The text of sample information should be filled into wells with a grey background in a pattern of Sample ID Sample Name Or you can click Open Sample Info button to load the existing Sample Flag File Step 4 Once you complete editing of the sample information click the Add Sample button to associate this information to the sample sequence Meanwhile the interface of the Sample Track page will be updated Step 5 Click the Save Sample Info button and then save the sample information on the current plate into a Sample Flag File for later use Step 6 CapitalBio Corporation Click the Delete button to clear all the information on the current plate Sample Info Saricie Tracking SS ___ _ _ a a eae Add Sample Save Samplelnfo n ojp o Ra o LLL D3 S7 QC7 Alnim k k d D B8 S10 QC10 1 C8 S11 QC11 D8 S12 QC12 B C T Le bd md mb me B9 513 0C13 C9 S14 QC14 D9 515 0C15 B10 S16 QC16 C10 S17 QC17
62. ide Spotting Warning Please make sure that the side with the bar code is up Before you lay down the slide please press the slide clasp away in order to avoid any scratch or damage to the slide Hold one narrow end of the slide with your fingers place the other narrow end onto the Slide Deck first press the slide clasp open carefully place down the slide into the slot with caution and release the slide clasp to grisp the slide The Slide Deck can accommodate up to 16 slides in a 2X 8 arrangement 5 4 4 Home Click the Home button to move the Robotic Arm to the home position at the top left corner of the Platform Ifany of cleaning operations are running the Home command will stop them 9 4 5 Load Pin Click the Load Pin button and the Robotic Arm will move the Spotting Module to the front of the instrument for conveniently loading the Pins PersonalArrayer 16 can be fitted with up to 4 Pins in a 2x2 arrangement Users can choose 1 2 or 4 Pins for Spotting Please refer to section 5 5 to check the locations of different combinations of Pins Warning The actual arrangement of the Pins in the Pin Holder should be consistent with the configuration shown in the software Otherwise it could lead to instrument malfunction damage run failure or contamination of the samples 5 5 Pin Configuration Click the Next button on the Prepare page or click the Pin Pin button on the left Task Panel to turn to the Pin Configuratio
63. iew sample tracking are provided on this page Please refer to sections 5 8 6 8 7 8 and 8 8 for instructions JE Clean 3 Run Hun For you to set up cleaning protocols for the Pin or Nozzle and save or load them In the Spotting mode the cleaning protocol can be composed of any combination of Rinse Sonicate and Dry operation In the Dispensing mode the protocol can be composed of any combinations of Rinse Exhaust and Dry operations Please refer to sections 5 9 6 9 7 9 and 8 9 for instructions Click the Run button on the left Task Panel to turn to the Run page The procedure to run a protocol is described below Step Check the protocol It is recommended to save Step 2 Click the Run button on the left Task Panel to turn to run page Step 3 Click the Start button Step 4 The software will check the program settings and prompt users if there is anything wrong Step 5 Confirm that the slides Pre spotting slides or plates are ready Step 6 Start to run the program Wash the Pins or Nozzle according to the protocol Step 7 Uptake samples according to the Sample Sequence Step 8 Pre spotting or Pre dispensing if the protocol requires Step 9 Spot or dispense according to array settings Step 10 Repeat steps 6 to 9 until all the slides or plates are finished During the procedure a user can click the Pause button to pause the current operation
64. iguration requirements Disk Space 40G or more CD ROM Drive 40 or faster of the computer Check the list and USB Controller USB 2 0 Display System 1 color display 1024 by 768 pixels Operating System Windows 2000 with Service Pack 4 or proceed Windows lt P with Service Pack 1 5 Setup PersonalArrayer16 1 0 Select Destination Location Where should Personal rrayerl 6 1 0 be installed O Setup will install Personal rrayer16 1 0 into the following folder To continue click Next If you would like to select a different folder click Browse C Program FilestCapitalBio Personal rrayerl 6 Step 5 Choose a destination directory for the installation At least 16 1 MB of free disk space is required fe Setup PersonalArrayer16 1 0 Select Start Menu Folder Where should Setup place the program s shortcuts r EY Setup will create the program s shortcuts in the following Start Menu folder Step 6 Specify a reference name for the program group which 1s about to be added into the Windows Start menu To continue click Next If uou would like to select a different folder click Browse ICapitalBio Personal rrayerl 6 CapitalBio Corporation 20 PersonalArrayer 16 Chapter 2 Software Installation ie Setup PersonalArrayer16 1 0 Select Additional Tasks Which additional tasks should be performed Select the additional tasks you would like Setup to perform while installi
65. ils of Cleaning Protocol files 3 4 2 Load Plates Click the Load Plates button and the Robotic Arm will move the Dispensing Module to the right extreme so you can place the slides onto the Plate Deck on the left side Please refer to section 7 4 2 for more details 8 4 3 Home Click the Home button to move the Robotic Arm to the home position the top left corner of the Platform If any of cleaning operations is running the home command will stop it 8 5 Dispenser Configuration Click the Next button on the Prepare page or click the Dispenser button on Wf Dispenser the left Task Panel to turn to the Dispenser Configuration page PersonalArrayer 16 currently has one Dispenser Nozzle Thus the combination cannot be changed 8 6 Plate Configuration HEP Plat Click the Next button on Dispenser Configuration page or click the Plate oe button on the left Task Panel to turn to the Plate page CapitalBio Corporation 74 PersonalArrayer 16 Chapter 8 Plate Dispensing Plate Info Plate Layout HGiFIE D C Bia OY O OLL LDO S S S S S S Users can specify the number OGOOGO OOd and location of the plates OGOOGO 5 You can decide which plate LOGO LOAD L will be printed first and how OO O OO OT many plates will be printed OO OO O In the Plate Dispensing OOOO OOOO mode Pre dispensing OOOO op returns excess sample back to OOOO DO OL the sample well so there 19 OOO OODODI no need to set up a Pre dispensing
66. io Corporation 79 PersonalArrayer 16 Chapter 9 Additional Software Features User Edo E Administrator Common Leer Add User Delete User Note There is an intrinsic account Administrator in the user list and it cannot be deleted 9 3 1 Add User Click the Add User button on the User Management dialog to pop up the Add User dialog Input the user name and password select a user group then click OK button to confirm it The new account will be shown in the user list Add User User Mame Printer Password ee H elope ee Group e User C Administrator Note The Blank space will be ignored Note User name and password must be completed CapitalBio Corporation 80 PersonalArrayer 16 Chapter 9 Additional Software Features 9 3 2 Delete User Select an entry in the user list in the User Management dialog and click the Delete User button to delete it 9 4 Reprint The procedure 1s as following 9 4 1 Step 1 Launch Click the Reprint button on the Run page when it is available to pop up the Reprinting dialog Reprint Start End Sample 1 B3 ka M3 7 Slide 2 3 w Y Array 11 9 p v W X Array 1 1 v Mw Replicate 1 i ones 9 4 2 Step 2 Configure Reprinting Scope Set parameters to define the scope for reprinting in the dialog including Define a range of samples by specifying the well to start with and the well to l aai end at
67. ion on the Pause amp Resume dialog or click the Stop button when the system is halted CapitalBio Corporation 54 Personal A rraver TM 16 Chapter 6 Slide Dispensing Chapter 6 Slide Dispensing 6 1 Overview The work flow and instructions for microarray dispensing onto slides with the PersonalArrayer 16 are described in this chapter After reading this chapter the user will have gained essential skills in instrument and software operatios for nSlide Dispensing procedures 6 2 Hardware Configuration In the Slide Dispensing mode the instrument should be equipped with the Dispensing Module on the Robotic Arm please refer to section 1 8 in the manual to switch between the Spotting Module and the Dispensing Module and the Slide Deck on the Platform please refer to section 1 9 in the manual to switch between the Slide Deck and the Plate Deck 6 3 Start the System Please refer to section 3 2 to start the PersonalArrayer 16 system The software will identify the current working mode and initialize the interface illustrated as below a Capital bio Personal Arr aver lp Slide Dispensing Prep me MZ CapitalBio PersonalArrayer 16 Work Flow Cleaning Operations Protocol of Cleaning UNA ALA nn E Rinse Protocol File Dispenser Rinse dan Y L Dispenser Dry Load Slide Hore Load Dispenser 6 4 Prepare The application software automatically begins with the Prepare page after launch CapitalBio
68. ior to switching to printing a new sample source and the number of washing cycles must be increased more when printing samples of higher viscosity or higher concentrations are used Note A stand alone Cleaning Protocol should be completed before shutting down the system to ensure complete cleanliness for subsequent use Emergency Stop Button The EMS Emergency Stop button can be found at the left side of the instrument It can be useful if the apparatus malfunctions or when you want to stop the instrument immediately Note The EMS button has to be reset before the microarray workstation can be restarted Service Service should only be conducted by a CapitalBio Corporation technician or by their authorized agencies Consult CapitalBio Corporation or authorized agencies for repair CapitalBio Corporation 7 PersonalArrayer 16 Safety Precaution instructions and technical support See Technical Support in the Prologue for more information CapitalBio Corporation 8 Personal A rraver TM 16 Chapter 1 Hardware Installation Chapter 1 Hardware Installation 1 1 Overview Please read the instructions in this manual carefully before you begin the installation and use of the instrument You should also be fully familiar with the operating procedures and requirements Please follow the installation guidelines fully and correctly to avoid damage to the instrument This chapter will describe hardware installation r
69. ispensing Provides detailed instructions on Plate Dispensing workflow Additional E me ahaa Provides descriptions of additional software features such as system self Software hoi check maintenance and Reprinting Features Routi TIRT l l l ae e Provides information on routine maintenance for quality service Maintenance Troubleshooting Provides answers to frequently asked questions and solutions to frequently encountered problems Technology amp Working Mode Technology PersonalArrayer 16 is a high performance microarray spotter It uses a precision system to distribute a specified quantity of liquid sample to specified position on the microarray substrate PersonalArrayer 16 uses precise robotic motion control technology to control the movement of X Y and Z axes and move the Spotting Pins or the Dispensing Nozzle to set positions to spot or dispense sample droplets and meet the requirements of high precision and high speed printing of microarrays CapitalBio Corporation 1 PersonalArrayer 16 Prologue PersonalArrayer 16 has both contact printing proprietary non contact dispensing technology This flexible technology enables PersonalArrayer 16 users to perform microarraying applications for nucleic acids proteins and other biomolecules on preformed chip surfaces such as glass slides plastic slides silicon slides plates or membranes The combined Dispenser or Pins cleaning system consists of sonicatin
70. ition Calibration to ensure the system functions correctly whenever any of the following occur a new system 1s installed the system is moved or changes are made to the hardware or software The configuration parameters are set to defaults immediately after installation Users can check them with help from technical support if necessary Please refer to Chapter 4 for more details 3 4 Position Calibration Position Calibration defines key positions for the operation of the instrument It must be performed before any printing job Please refer to 4 2 for more details 3 5 Printing Preparation Click the Prepare button on the left Task Panel to turn to Prepare i Prepare aie On the Prepare page the user can send commands to the instrument to rinse dry sonicate and exhaust the pins or nozzle to switch decks or modules and to send the Robotic Arm to the home position Users can load an existing stand alone Cleaning Protocol to simplify the daily routine as follows Step 1 Input the path name of the protocol file in the text box or click the Open button to browse and select Step 2 Click Start button Step 3 The progress bar indicates the task is running Step 4 Wait for the task completion or click the Stop button to break it You can set up a wash protocol on the Clean page and save it for later use The wash protocol can be complex Please refer to 5 9 6 9 7 9 and 8 9 for detailed operations 3 6 Program In order t
71. ition page or click the Sample button on the left Task Panel to turn to the Sample Sequence page A graphical interface simulating a 384 well plate or a 96 well plate when in the Dispensing mode is presented to set up the Sample Sequence for sample uptake Please refer section 6 8 for more details When the sample plate type changes please refer to section 4 2 7 to calibrate its position 8 9 Cleaning Protocol TCC CI Click the Next button on Sample Sequence page or click the Clean Rat button on the left Task Panel to turn to the Cleaning Protocol page Please refer to 6 9 to set up the Cleaning Protocol 8 10 Run Click the Next button on the Cleaning Protocol page or click the Run button on the left Task Panel to turn to the Run page Click the Start button to run the protocol 8 10 1 Run Page Layout Plate Info Sample Plate 1 HGF ED CBA HGF EDC BA 00000000 00000000 00000000 0000000013 000000001 l 00000000 000000005 00000000 000900001 00000000 90030000 TF 0000000011 010101010101010 F 0000000012 Well Plate 2 X Array 6 Time Elapsed Time Left Reminder lt Back B The Plate Info section reveals the current status of plates including the current sample the current plate and 1f Array Replication is applied It also indicates the row index and column index of the current ar
72. l incidental indirect or consequential damages and or losses including but not limited to profit loss operation interruption business interruption business information loss and any other pecuniary loss arising from the use of this System or inability to use this System CapitalBio does not guarantee the stability of this System if you install other software in the process of using this System on the same computer This System may only work and function properly under correct usage protocols CapitalBio s total liability to you for any damages and or losses for any causes whatsoever under the terms of this Agreement will be limited to the actual amount paid by you for this System Termination of License If you breach any terms or conditions of this Agreement CapitalBio shall have the right to terminate the license at any time If CapitalBio decides to terminate this license you must immediately destroy no more than three 3 days after the termination this System and any copies of any documents of this System or return them to CapitalBio Applicable Laws This System shall be protected by the Copyright Law of the People s Republic of China and relevant international intellectual property protection treaties which have been acceded to and enforced in the People s Republic of China This Agreement shall be governed by the laws of the People s Republic of China If you have any question with respect to this Agreement ple
73. late when in Dispensing mode 1s presented to set up the Sample Sequence for sample uptake Whenever you change the plate type please refer to section 4 2 7 for instruction on how to calibrate the sample plate position on the System Configuration dialog The procedure is described below 6 8 1 Step 1 Specify Sample Wells on the Virtual Plate Please refer to section 5 8 6 8 2 Step 2 Plate Sequence Please refer to section 5 8 6 8 3 Step 3 Edit the Sample Sequence List Please refer to section 5 8 6 8 4 Step 4 Advanced Options Click the Advanced Option button to bring up the Advanced Sample Option dialog box and configure a set of parameters The parameters are organized into two pages Dispensing Settings and Uptaking Sample Dispensing Settings Uptaking Sample Sample Inex Priority Dispensing Settings Uptaking Sample Row Column Y Row gt Col C Col gt Row Dispensing Timefmicrosecond Channel 1 250 Channel 2 Hele Left Right f Right gt Left Channel 3 Channel 3 Aspiration Mode Full Sample Dry Times after Aspiratin 1 The Row Column option and Row option have been explained in section 5 8 1 The Dispensing Time for each spot on the substrate in us At Dispensing Time present time PersonalArrayer 16 supports only one nozzle so only the first text box is available Refers to Aspiration Mode for sample and can be selected from two alternatives Full Sample mode and Partial Sample mode
74. latform consists of a multi axis Robotic Arm a platen a Humidifier Rinse amp Dry module and Sonicator The Robotic Arm is responsible for precise positioning of the pin nozzle The X axis refers to left and right the Y axis refers to forward and backward in the horizontal plane and the Z axis refers to upward and downward The platen carries Plate Deck or Slide Deck to spot on various substrates The Rinse amp Dry module is connected to the peristaltic pump and the vacuum pump to rinse and dry the Pins or Nozzles The Sonicator implements sonicleaning of the Pins in the Spotting mode or is used as a System Liquid container in the Dispensing mode The Sample Plate accommodates samples for printing and it should be either a monolithic 96 well plate or 384 well plate The Humidifier is used to maintain a constant relative humidity for the working space within the instrument CapitalBio Corporation 12 PersonalArrayer 16 Chapter 1 1 4 4 Front panel Hardware Installation There are 6 LED indicators on the Front panel as shown below Power Peristaltic Pump Dry Error Humidifier Sonicate LED status description LED Status Indication Power ON Instrument is power on OFF Instrument is power off Error ON EMS is pressed down or other errors occurred OFF Other circumstance Humidifier ON Humidifier is working OFF Humidifier is idle Sonicator ON Sonicator is working OFF Sonicator is
75. leaning Protocol has three steps Rinse Exhaust Dry The number of cycles of this iteration is dependent on the sample characteristics Samples with high viscosity require more cycles and an elongated time span It is recommended to optimize the Cleaning Protocol by conducting a remnant fluorescence test prior to full state usage Please refer to section 5 9 to set up the Cleaning Protocol The user can click the Save button to backup the current protocol or click the Open button load an existing protocol Please refer to section 5 4 2 for more details CapitalBio Corporation 61 PersonalArrayer 16 6 10 Run Slide Dispensing Click the Next button on the Cleaning Protocol page or click the Run button on the left Task Panel to turn to the Run page Click the Start button to run the protocol 6 10 1 Run Page Layout Slide Info Sample Plate 1 DOI aaa a ma 9 RRR RR RSS l i 1 8 ma fh ts aa f rh a IIE 2 3 5 y a DIM dl i LE lG a EE SER y HE eR 1 g IIT TR g 10 mmj an 11 a ron Slide Z F S H k L M H r p F The Slide Info section reveals the current status of the slides including the current sample current slide and if the Array Replication is true the row index and column index of the current array and the index of the current replicate The Sample Plate section illustrates the status of the current sample plate including the plate index which wells have alr
76. lect the sample well from the sample sequence The ordinal number will be automatically updated A Click the Select All button to select all wells into the sample sequence The numbering rule applies in the same way with rectangle selection Click the Clear All button to deselect all the wells from the sample sequence ES H TI LT 2 3 SEE Numbering AJR Bia A 00 l 158 AJ Ee AJ ia Fic e MAA 1618989891 E AAH 6189898 Cien caama 6c caama Row Column Row gt Col Col gt Row Row gt Col Col gt Row Row Left gt Right Left gt Right Right gt Left Right gt Left CapitalBio Corporation 41 PersonalArrayer 16 Chapter 5 Slide Spotting 5 8 2 Plate Sequence Users can manage the plate sequence as following Input an ordinal number for the plate which is about to be added into the plate sequence in the text box Input a copy number for the plates which are about to be added into the plate sequence The corresponding number of replicates sharing the same sample well arrangement and numbering will be added to the list in a batch Select where the current plate design will be added Select Append to add the current plate design to the end of the Sample Sequence list represented in the list box on the right hand side Select Insert to add the current plate design in front of the selected items in the Sample Sequence list or to add it to the end 1f there is no selected item in the list After finishing t
77. ll turn off Click the Pin Dry button the vacuum pump will start to work and w Pin Dry the Robotic Arm will dip the Pin into the Vacuum Slot to get rid of remaining liquid Meanwhile the Dry Indicator will be illuminated Click the Pin Dry button again to exit the current action The Dry Pin D Y ins Indicator will turn off 9 4 1 5 Sonicate O Sonicate Click the Sonicate button the Sonicator will start to ultrasonically agitate the water bath The Sonicate Indicator will be illuminated sonicate Click the Sonicate button again to exit the current action 5 4 1 6 Pin Sonicate 2 Pin Sonicate The Sonicate Indicator will turn off Click the Pin Sonicate button the Sonicator will start to ultrasonically agitate the water bath with ultra sound pulse and the Robotic Arm will dip the Pin into the bath The Sonicate Indicator will be illuminated Pin Sonicate 5 4 2 Cleaning Protocol Click the Pin Sonicate button again to exit current action The Sonicate Indicator will turn off Users can load a Cleaning Protocol from existing files to run a procedure consisting of a series of actions Please refer to section 5 9 for details on Cleaning Protocol files 5 4 3 Load Slides Click the Load Slides button and the Robotic Arm will move the Spotting Module to the extreme right so you can place the slides onto the Slide Deck on the left side CapitalBio Corporation 4 PersonalArrayer 16 Chapter 5 Sl
78. m You are not permitted to use the copyrights specified in the paragraph above If this System contains documents only in electronic format you may print copies of the documents You may not delete any copyright statements of this System You warrant that you will copy any copyright statement when you make a copy of this System or any portion of this System in accordance with this Agreement You agree to refrain from doing any illegal copying of any forms of this System and or any parts of this System Post Sales Warranty CapitalBio warrants that within ninety 90 days after the selling of this System this System shall not have any material defects or technical defects subject to the condition that this System is used in its normal manner of operations In the event that a defect is confirmed by CapitalBio CapitalBio only shall be responsible for replacing the defective software This is the only remedy available for you If the defect is caused by or arising from any accident abuse or mistake the above mentioned post sales CapitalBio Corporation II PersonalArrayer 16 warranty shall be invalid Exemption from Liability Except for the contents specified in the above paragraphs you shall not have any other post sales watranties of this System Limitation of Liability Subject to the scope of applicable laws specified in this Agreement in no event shall CapitalBio and its agents and sales persons be liable for any specia
79. m will lift up the Nozzle out of the basin The Rinse Indicator will turn off Click the Dry button and the vacuum pump will start to work Meanwhile the Dry Indicator will be illuminated Y Dry 6 4 1 4 Dispenser Dry Dispenser Dry Click the Dry button again to exit the current action The Dry Indicator will turn off Click the Dispenser Dry button the vacuum pump will start and the Robotic Arm will dip the Nozzle into the Vacuum Slot to get rid of remaining liquid Meanwhile the Dry Indicator will be illuminated Dispenser Dry 6 4 1 5 Exhaust Click the Dispenser Dry button again to exit the current action The Dry Indicator will turn off Click the Exhaust button the Robotic Arm will move the Nozzle directly over the Rinse Basin turn on the valve in the Dispensing Exhaust ka Sang Module and Exhaust the Nozzle and the tubing connected to the Nozzle Ly Exhaust Click the Exhaust button again to exit the current action 6 4 2 Cleaning Protocol Users can load a Cleaning Protocol from existing files to run a procedure consisting of a series of actions Please refer to section 6 9 for details on Cleaning Protocol files 6 4 3 Load Slides Click the Load Slides button and the Robotic Arm will move the Dispensing Module to the right extreme so you can place the slides onto the Slide Deck on the left side Please refer to section 5 4 3 for more details 6 4 4 Home Click the Home button to move t
80. move the Spotting Module or the Dispensing Z Down Module along the Z axis a step per click X to Calibrated Pos Click the button to move the Spotting Module or the Dispensing Y to Calibrated Pos Module along the X Y Z axis to the position calibrated for the last Z to Calibrated Pos time eid Click the button to move the Spotting Module or the Dispensing Y Home l be 7 Home Module along the X Y Z axis to home position 0 0 0 Note Whenever a new system is installed or the system is moved to a new place or some changes are made to the hardware or software it is mandatory to check the configuration parameters It 1s especially important to perform Position Calibration to ensure that the system functions correctly and to avoid any potential damage Please check and confirm that the step length per jog is not too large Set it to appropriate values in order to prevent any collision or other damage 4 2 1 Rinse Position Calibration The Rinse Position is where the inlet of the Rinse Basin is located It is necessary to calibrate the Rinse Position to ensure that all 4 pins on the Pin Holder or the Nozzle can descend into CapitalBio Corporation 29 the inlet of the basin Please refer to 1 10 to see the basin s location in the instrument The procedure is the following Step 1 Select the Rinse Select the Rinse option in the Positions section The X Y Z coordinates that were last calibrated will be shown in the
81. n page Combination Pattern CapitalBio Corporation PersonalArrayer 16 provides four combinations of Pin arrangements in the Pin Holder 1x1 1x2 2x1 2x2 Users El B can choose the combination in the combo box and preview it in the box below Note Please confirm that the actual arrangement of the Pins in the Pin Holder is consistent with the configuration in the software If you change the pin configuration the array specifications and plate specifications will become invalid and you will have to check and reset them again 42 PersonalArrayer 16 Chapter 5 Slide Spotting 5 6 Slide Configuration Click the Next button on the Pin Configuration page or click on the Slide DS Slide button on the left Task Panel to turn to the Slide page This page consists of two sections the Spotting Area section and the Slides Info section Spotting rea Unit rmnm Users can define the dimensions of the printable area of the slides in the Spotting Area section Width length of the slide The currently supported dimensions are 25mm X 75mm LX LY Margins between the edges of the printable area and the edges of the slides OX OY No less than the Min Margin which could be set on the advanced slide option dialogue refer to the last part of this section Slide Info Slide Layo ut In the Slides Info section the user can specify the number and location of the slides and the Pre spotting Slide
82. nal A rraver TM 16 Chapter 7 Plate Spotting Array Preview 4 Direction Y Direction H LE F E D E A First Array Position la 1 na 1 Spot Distance 300 300 micron a Spot Count per Pin 3 Max Spot Count Replicate per Sample Multi Array Array Separation Well Count Array Count I Y Direction Fa Lp Ch 1 oo Max Array Count Array Replication Yes Pre Spatting Pre Spatting Count Pre spotting N N LLL SOCCOOCOCO sO OOOOO OO SOCCOCOCOCO oO OOOO OO 90000000000 0000000009 Lim OOOO OOOOOOOO Distance micron lt Back B N etn 3 On this page users can customize the number of arrays that will be printed on the plate how many spots will be in an array and how the arrays and spots are arranged Users can preview the arrangement on a virtual plate in the box on the right In Plate Spotting mode each array will occupy a well on the plate First Array Specify which well on the plate the first array will locate in The first array in a Position block of arrays is defined as the top left corner of the block Spot Center to center spot distance within an array in umbetween two consecutive P deposition actions taken by the same Pin It usually ranges from 180um Distance 400um dependent upon the diameter of the spot The number of depositions made by the Spotting Module specifically the Spot Count E er Pin number of spo
83. ng Personal rrayerl 6 1 0 then click Next Additional icons Create a desktop icon Step 7 Choose whether to create a shortcut on the desktop fe Setup PersonalArrayer16 1 0 Ready to Install Setup is now ready to begin installing Personal4rrayer16 1 0 on your computer Click Install to continue with the installation or click Back if you want to review or change any settings Destination location C Program Files CapitalBio sPersonal4rrayer1 6 Step 8 Start Menu folder s s CapitalBio Personal rrayerl 6 C onfirm the installation task s Additional tasks Click Install button to start Additional icons Create a desktop icon fe Setup PersonalArrayer16 1 0 Installing N Please wait while Setup installs Personal rrayer16 1 0 on pour computer E Extracting files C Program FilestCapitalBio Personal rrayerl EXMFC 1 dl Step 9 The progress bar for the installation 5 Setup PersonalArrayer16 1 0 Completing the PersonalArrayer16 1 0 Setup Wizard Setup has finished installing P l rrayer16 1 0 aia The anal A ri by selecting the Step l 0 installed icons Installation is complete and click Finish to exit the wizard You can choose to reboot the system immediately or later Click Finish to exit Setup View Personal rrayerl6 Help Document CapitalBio Corporation 21 PersonalArrayer 16 Chapter 2 Software Installation Note With the help of setup
84. ntact the technical support at CapitalBio 11 2 Problem and Solution Solution Cause 1 3 Z axis no response Motor power failure Please contact CapitalBio Bad USB connection Check USB Connection ida Check power supply Starting Emergency Stop is pressed Check the Emergency Stop or Enclosure is open and close the Enclosure Launch failed l l l System configuration file 19 configuration file E Reinstall the software et missing or damaged missing Pin s cannot be Dirty environment Improve the air cleanliness raised or dropped causing Pin or Pin hole class clean the pins smoothly contamination with Sonicator ee ee Replenish the Wash Buffer Bubbles in Rinse Bucket Basi Fluid tube d gR Wa n Taan Replace the tube peristaltic pump Rinse Basin Waste Bucket is full Empty the Waste Bucket overflowing Outlet conduit is too high Lower the conduit down e Check it and rerun Position Bad Position Calibration s S Calibration if necessary Abnormal exit from Motion module exception Restart the instrument and running job l l software program If it does not Dispensing Running work please exception f f PE contact CapitalBio Repeat stand alone Cleaning Protocols and refer to Safety inside air course of i i l l l Precaution to check available No intake during dispensing module S SR Uptake Insufficient Sample Increase Sample aspiration Excessive sample viscosity Insufficient sam
85. o plan a printing run the following steps and corresponding command interfaces are involved Available in the Spotting mode For you to specify the amount of Pins r Pin on the Pin Holder and the pattern in which the Pins are arranged Please refer to sections 5 5 and 7 5 for instructions Available in the Dispensing mode Only 1 nozzle can be applied to Hf Dispenser the PersonalArrayer 16 Please refer to sections 6 5 and 8 5 for Instructions Available in Slide Spotting or Slide Dispensing mode For you to HEE Slide specify the printable area on the slides the number of slides the start slide and the number of pre spotting slides in Slide Spotting mode Please refer to sections 5 6 and 6 6 for instructions CapitalBio Corporation 24 PersonalArrayer 16 Chapter 3 Software Tutorial Available in Plate Spotting or Plate Dispensing mode For you to specify the number of plates and which is the start plate Please refer to sections 7 6 and 8 6 for instructions For you to specify the arrangement of the microarrays such as the array parameters and spots on the slides or in the plate well replication of the spots and arrays pre spotting and pre dispensing settings Please refer to sections 5 7 6 7 7 7 and 8 7 for instructions For you to specify the number of sample plates sample distribution among the wells and sampling sequence In addition access to Sample the Advanced Option related to sample prev
86. ocessing and grey for samples yet to be processed The Progress section describes the progress on various levels with bars including the time statistics and an estimation of the Pre spotting progress Spotting progress and plate progress An information section 1s also available in this section There are control buttons at the bottom of the page including Start button Pause button Stop button and Reprint button We will continue to discuss Pause button and Stop button below Please refer to section 9 4 to learn more about Reprint button 7 10 2 Pause and Proceed The pause and resume functions are provided to handle unexpected emergency events particularly during Spotting applications Please refer to 5 10 2 for more details 7 10 3 Stop You can either select the Exit option on the Pause amp Resume dialog or click the Stop button when the system is halted CapitalBio Corporation 71 PersonalArrayer 16 Chapter 8 Plate Dispensing Chapter 8 Plate Dispensing 8 1 Overview The work flow and instructions for microarray Dispensing onto plates with the PersonalArrayer 16 are described in this chapter After reading this chapter the user will have gained essential skills in Plate Dispensing procedures and for instrument and software operation 8 2 Hardware Configuration In the Plate Dispensing mode the instrument should be equipped with the Dispensing Module on the Robotic Arm please refer to section 1 8 in this
87. on Calibration ooononooonononoconononconocnoncconononcnnnnnocacacenidociccccccanacad naso 35 43 Disponse TET RIE 35 A A sash E E pe E A E cons eased aac sauce ere aie teem canes 37 OB ER O a a a of dsesstneetoawoalseensesetectaet es 37 Chapter Di IS PO ET 39 Dib S 39 52 Hardware AAA S ES 39 SS ET eD TT 39 DE T CPP E ESTE O A TA eer eee ee eee 39 E O T Te T 40 S C leanne OO C ON date tect ts atta hata te ela id o clases 41 IA A A line toes Sion a EE tata eeibtydabegtebees 41 K P1O MIG aeRO EEE ETE ET E E N E Mecpae mea touceteas 42 54S Load Pihisersierecosi ara aana N E A E N 42 A nscale eientiaasi med ncadie atu eiantieaneteodiea 42 0 dE CON i Sal OM sai a a aadau aeiaea sarees ede aed 43 ITANA DEA 6 Meee H 44 DO AMPS SCO CIC maes 46 5 8 1 Specify Sample Wells on the Virtual Plate ooocccccncnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnss 47 5 8 2 Ie UT 48 5 6 3 Edit the Sample Sequence cS TT 48 DO eA IN A A E 48 ee I PTE VI OW CP nation set toate O II A 49 O E O 51 ON 51 LO 1 RUN Pape La OU A eee 52 IAO Pau eand Proc deea e diodo leticia 52 SL T PAEA i rec i te eames i ee ie E A he eee ie tees he tte EA P E S E EE A AOA 54 Chapter OS Ges PCS TTT 55 O OVER VICW iia 55 6 2 Hardware Con oura On T 55 SR Olam LNCS AAPP R 55 PP O er ne nC 55 CapitalBio Corporation II PersonalArrayer 16 s 1 Oper eene S S6 AO A Protocol A A ae eaaiass Matias macte cae aose 57 GeO OOO 57 Or FTO aE E
88. on the left Task Panel to turn to the Cleaning Protocol page The procedure to set up a Cleaning Protocol is the same as in the Slide Spotting mode Please refer to section 5 9 for more details 7 10 Run Click the Next button on the Cleaning Protocol page or click the Run button on the left Task Panel to turn to the Run page Click the Start button to run the protocol 7 10 1 Run Page Layout Plate Info HGFEDCBA HGFEDCBA 000000001 00000000 000000001 00000000 3 000000004 l 00000000 000000005 00000000 00090000 s 000000001 10 C0 3500 Wh ES 0000000010 0000000011 2000000017 2000000012 Well Plate 2 X Array 1 Time Elapsed Time Left Reminder The Plate Info section reveals the current status of plates including the current sample current plate and 1f Array Replication is applied It also indicates the row index and column index of the current array and the index of current replicate The Plate section illustrates the status of current sample plate including the plate index which CapitalBio Corporation 70 PersonalArrayer 16 Chanter 7 Plate Spotting wells have already been sampled which ones are being currently sampled and which ones have not yet been sampled The wells at different status levels are differentiated by different colors Green for processed samples blue for the samples in pr
89. or performance of procedures other than those specified in the installation guide and user manual may result in damage to the instrument loss of data invalid data hazardous voltage moving parts or even cause fire Exposure to hazards may cause severe or fatal injury Certification Identification and Power Supply Label PersonalArrayer 16 Rae gre Microarray Spotter L CapitalBio ret Corporation INPUT RATING AC 100 240V 50 60Hz 1A CATALOG NUMBER 11007X CAPITALBIO CORPORATION SERIAL NUMBER 110 0XXX 18 Life Science Parkway MANUFACTURE DATE Changping District Month Year Beijing 102206 China el 86 10 80726868 Month Year S Hie i HE http www capitalbio com AR 11007X SN110 0XXX A This device complies with Part 15 of the FCC Rules Operation is subject to the following two conditions 1 this device may not cause harmful This Class A digital apparatus complies with interference and 2 this device must accept any Canadian ICES 003 interference received including interference that Cet appareil num rique de la classe A est may cause undesired operation conforme a la norme NMB 003 du Canada MADE IN CHINA Product Label Enclosure The Enclosure is designed to protect users from exposure to hazardous moving parts or electric shock Users are not supposed to access the interior of the PersonalArrayer 16 during routine operations Please do not lift the Enclosure open while the instrument is running
90. ould be no less that 8L A pressure regulator should be connected to the source to output 0 3 0 4 MPa pneumatic pressure PU tubing with 4mm outer diameter connects the pressure regulator to PersonalArrayer 16 The tubing should not be too long Warning O The output pressure range of the regulator should be 0 3 0 4 MPa but never higher than 0 5 MPa Please observe these regulations to avoid risk of instrument damage or injury Please recharge the cylinder when its output is lower than 1 MPa The storage and operation should comply with all local safety regulations CapitalBio Corporation 10 PersonalArrayer 16 Chapter 1 Hardware Installation 1 3 Receiving Inspection 1 3 1 Initial Inspection upon Receipt of Equipment Please check the package as soon as you receive it If you find any obvious damage during your visual inspection describe it on the receipt sheet that comes with the package 1 3 2 Unpacking If you find any damage of the instrument itself after you remove all the packaging please report this immediately to the delivering agent and CapitalBio Corporation Please avoid violent shaking and collision when you move and place the instrument Please check if the components are all present after opening the packing boxes Please contact CapitalBio if you have any questions or concerns Please do not connect the instrument to a power supply if you notice any obvious damage 1 3 3 Packing List
91. pare The application software begins with the Prepare page automatically after launch Alternatively you can click the Prepare button on the left Task Panel to go to the Prepare CapitalBio Corporation 65 PersonalArrayer 16 Chapter 7 Plate Spotting page Users can load the Pin s onto the Pin Holder load plates on the Plate Deck clean the Pin s and move the Robotic Arms to the home position Warning Please carry out Position Calibration before you proceed 7 4 1 Cleaning Operations During the cleaning operations users can take the following actions Rinse Pin Rinse Dry Pin Dry Sonicate and Pin Sonicate The cleaning operations in the Plate Spotting mode are the same as ones in the Slide Spotting mode Please refer to section 5 4 1 to learn more Users can load a stand alone Cleaning Protocol from existing files to run a procedure consisting of a series of actions Please refer to section 5 9 for details of cleaning protocol files 7 4 2 Load Plates Click the Load Plates button and the Robotic Arm will move the Spotting Module to the right extreme so you can place the slides onto the Plate Deck on the left side Press the narrow end with the alphabetical index of the plate against the clasp on the Plate Deck and push it into the slot The Plate Deck provided by the PersonalArrayer 16 can accommodate up to two 96 well plates Warning Please make sure that the narrow end with the alphabetical index of t
92. peration and keep the instrument idle If the Clean before resume box is checked a cleaning operation will be executed prior to any further action when you want to resume the protocol Backward Choose to return to a certain prior step and repeat the protocol You can specify various references to indicate where you want to reprint Sample Specify an index number to determine which sample will be reprinted Slide Specify an index number to determine which slide will be reprinted Specify an index number to determine which array along the Y axis will be Y Array reprinted If there are no replicate arrays in the protocol this reference will not be available Specify an index number to determine which array along the X axis will be X Array reprinted If there are no replicate arrays in the protocol this reference will not be available Replicate Specify an index number to determine which replicate will be reprinted CapitalBio Corporation 53 PersonalArrayer 16 Chapter 5 Slide Spotting Forward to the last position Choose this option to resume from where the user halted the process and returned to the previous step The option is only available after pause and return Click the OK button to execute the corresponding operations If the system is halted the Pause button will appear as the Continue button and the user can click it to resume the current protocol 5 10 3 Stop You can either select the Exit opt
93. ple volume Excessive Sample Decrease Sample aspiration aspiration time time Excessive Air aspiration time Contamination or dust 5 6 Bubble in Nozzle and nearby tube Decease Air aspiration time gt ed ta a a a a d eS N U P CapitalBio Corporation 87 PersonalArrayer 16 Chapter 11 Troubleshooting Improve air cleanliness class Dust clot in the Nozzle repeat stand alone Cleaning Protocols DE suspended Insufficient Dispense under the Nozzle Increase Dispense pressure pressure Insufficient sample uptake Replenish the sample well Nozzle failure Please contact CapitalBio E Insufficient humidity Increase humidity 3 1 Missing spot S impaired pin drop Excessive sample viscosity Decrease sample viscosity Excessive velocity Decrease velocity Irregular feature Adjust the Pin Holder to be Uneven Pin Holder parallel to the Platform with spirit level 3 3 Overlapping spots Deficient pre spotting Increase Pre spotting Count Disordered arrav Excessive velocity or loose 3 4 y 9 Please contact CapitalBio formation components Spotted l I Sample aspiration E Insufficient sample uptake E Buga Beat arrays Uneven spot size time during the run Increase sample uptake Excessive sample viscosity frequency Cover and seal the Vacuum Increasing spot l Slots that are not in use with i l Deficient vacuum l intensity as running plastic membrane to improve vacuum efficiency P
94. poration 32 PersonalArrayer Y 16 Chapter 4 Configuration Note When you are calibrating target plate position there should be only one Pin on the Pin Holder if it is in the Plate Spotting mode The procedure goes as follows Step Select Target Plate Select H1 Well Target options in the Positions section The most recent calibrated X Y Z coordinates will be shown in the Calibrated Pos Parameters section and the current X Y Z coordinates of the Spotting Module or the Dispensing Module will be shown in the Current Pos Parameters section Step 2 Confirm initial position of the Robotic Arm The initial position will be in the upper left extreme after the instrument is power on that is 0 0 0 in the Current Pos Parameters section Please check if the Robotic Arm is actually at 0 0 0 If it 1s not click the X Home or Y Home or Z Home button to move along the corresponding axis Step 3 Calibrate and save the X axis and the Y axis coordinates CAUTION In the Jogging section set the step for the X axis and Y axis to the appropriate values and click the buttons to move the Spotting Module or the Dispensing Module to hover over the center of H1 well Specify that the X Y coordinates will be saved in the check boxes within the Current Pos Parameters section Click the Save button and then confirm to use the current position as a new calibrated position Step 4 Calibrate and save the Z axis coordinates CAUTION
95. radiating large electromagnetic emission such as pacemakers electric welding equipment etc O Keep the instrument away from power consuming appliances that frequently start up or turn off such as refrigerators and centrifuges Keep the instrument away from any other strong magnetic fields Do not share the power strip with too many other electrical appliances Do not plug in or remove any other equipment connected to the same power strip while the instrument 19 running Note An EMC environment compliant to CE regulation is required 1 2 5 Computer Workstation The computer configuration should meet the following requirements to guarantee the software performance for PersonalArrayer 16 CPU Pentium 4 2 0GHz or higher Physical Memory 512M or more Virtual Memory 512M or more Free Space on Hard disk 40G or more CD ROM 40x speed or faster USB Controller USB 2 0 Display System 17 inch colored with resolution of 1024x768 pixels or more Microsoft Windows 2000 patched with Service Pack 4 or Operating System Microsoft Windows XP patched with Service Pack 2 1 2 6 Pressure Supply requirements An independent pneumatic pressure source is required for PersonalArrayer 16 in Dispensing working mode The source can be either purified compressed air nitrogen cylinder or purified air compressor The compression resistance of the cylinder should be no less than 14 MPa and inner volume of the bottle sh
96. ray and the index of current replicate The Plate section illustrates the status of current sample plate including the plate index which wells have already been sampled which ones are being sampled right now and which ones have not yet been sampled The wells at different status levels are differentiated with different CapitalBio Corporation 71 PersonalArrayer 16 Chapter 8 Plate Dispensing colors Green for processed samples blue for the samples in processing and grey for samples yet to be processed The Progress section describes the progress on various levels with bars indicating the time statistics and estimation of the Pre dispensing progress Dispensing progress and plate progress An information section is also available in this section There are control buttons at the bottom of the page including the Start button Pause button Stop button and the Reprint button We will continue to discuss Pause button and Stop button below Please refer to section 9 4 to learn more about the Reprint button 8 10 2 Pause and Proceed The pause and resume functions are provided to handle unexpected emergency events particularly during Dispensing applications Please refer to section 6 10 2 for more details 8 10 3 Stop You can either select the Exit option on the Pause amp Resume dialog or click the Stop button when the system is halted CapitalBio Corporation 78 PersonalArrayer TM 16 Chapter 9 Additional Software Feature
97. rea and Min Margin MAULI the edge of the slide OX and OY should not be less than the Min Margin Cancel 6 7 Array Definition Click the Next button on the Slide page or click the Array button on the left Task Panel to turn to the Array Definition page CapitalBio Corporation 58 PersonalArrayer 16 Array Spot Distancefmicron Spok Count per Channel Max Spot Count Replicate per Sample Multi Array Array Separationkmen Array Count Max Array Count Array Replication A Direction 1000 Z iil A Direction il BS E Y Direction Y Direction pean m Preview Slide Dispensing Pre Dispensing Pre Dispensing Count Pre dispensing Timetmicrosecond Pa C LK lt Back B N evt gt In this page users can customize how many arrays will be printed on the slide how many spots will be in an array and how the arrays and spots are arranged Users can preview the arrangement on a virtual slide in the box on the right Spot Distance Spot to spot distance within an array in um It 1s dependent upon the diameter of the spot usually 800um 1500um Spots Count The number of deposition action taken by the Dispenser specifically the number of spots printed by the Dispenser within an array It should not be peri aanne greater than the Max Spot Count The maximum number of spots is mainly dependent upon the dimensions
98. rovide temperature and Environment substrate humidity guarantee improve sample quality factors air cleanliness class optimize sample preparation process Deficient humidity Increase humidity utili Noze Repeat stand alone Cleaning Protocols s Electrostati h accumulation Poor quality spots The Nozzle is too far awa 7 Decrease the distance from substrates Increase Dispense pressure pressure l l Increase the Exhaust frequency Tiny bubbles in the tube RTT Bubbles or foam in sample Eliminate them centrifuge Overlapping spots soni oun Improper dispense Decrease Dispense pressure Insufficient sample uptake Increase sample uptake Dispensed arrays 34 3 6 de 4 1 4 2 3 l Insufficient Dispense Uneven spot size Increase Dispense pressure 4 i pressure after a while Insufficient Dispensing Increase Dispensing Time up Time to 250us CapitalBio Corporation 88 PersonalArrayer 16 Chapter 11 Troubleshooting Excessive velocity or loose l components Substitute substrates or apply proper substrate surface modification Disordered array formation Incompatible substrates for Dispensing Failed to load file when click the Open Sample Please refer to section 5 8 to Info button on T a modify the file and retry the Sample Tracking dialog File Operation Select a file in a compatible Incompatible file format format or edit the current protocol and sa
99. rrent X Y Z coordinates of the Spotting Module will be shown in the Current Pos Parameters section Step 2 Confirm initial position of the Robotic Arm The initial position will be in the upper left extreme after the instrument is power on that is 0 0 0 in the Current Pos Parameters section Please check if the Robotic Arm is actually at 0 0 0 If it is not click the X Home or Y Home or Z Home button to move along the corresponding axis Step 3 Move to the proper position along the X Y axis and save In the Jogging section set the step to the appropriate values for the X Y axis and click the buttons to move the Spotting Module directly over the upper left corner of the Pre spotting Slide Specify that the X Y coordinates but not the Z coordinate will be saved in the check boxes within the Current Pos Parameters section Click the Save button and then confirm to use the current position as a new calibrated value Step 4 Move to the proper position along the Z axis and save In the Jogging section set the step to the appropriate value for the Z axis and click the buttons to move the Spotting Module to make the Pin barely contact with the surface of the slide Specify that the Z coordinate but not the X and Y coordinates will be saved in the check boxes within the Current Pos Parameters section Click Save button and then confirm to use the current position as a new calibrated value The Spotting Module will move up
100. s Chapter 9 Additional Software Features 9 1 Overview PersonalArrayer 16 provides additional functions including instrument Self Check Reprinting and User Management The Self Check function is used to run tests to check whether the instrument 1s in normal condition and reset the instrument to initial status Reprinting is actually used to selectively run part of the protocol You can specify a smaller range of samples slides or plates arrays and replicates in the programmed protocol The user can make use of this function to Reprint the missing spots after the running protocol is completed or just select part of protocol to run For example a collection of samples with tag information already filled 1n In the User Management dialog You can control the user entry including privileges and passwords 9 2 Self Check Click the Self Check button on the system panel which is on the right top qe corner A dialog will pop up for you to confirm T After Self Check is completed the Robotic Arm will be moved to the home position 9 3 User Management g Click the User Management button on the system panel which is on the right top corner The User Management dialog will pop up All registered user entries will be listed in the User Management dialog You can append items to the list or remove items from the list Note Only users in the Administrator User Group can access the User Management dialog CapitalB
101. sition which should be above the plate Step 3 Move to the proper position CAUTION In the Jogging section set the step to the proper value for the Z axis and click the buttons to move the Nozzle directly over the plate top surface about 2mm above CapitalBio Corporation 34 PersonalArrayer 16 Chapter 4 Configuration Step 4 Save the calibrated position CAUTION Specify that the Z coordinate but not the X Y coordinates will be saved in the check boxes within the Current Pos Parameters section Click the Save button and then confirm to use the current position as a new calibrated value The Dispensing Module will move up to the home position along the Z axis 4 2 9 Pre spotting Slide Position Calibration In the Plate Spotting mode it is necessary to calibrate the Pre spotting Slide position The X and Y coordinates represent the upper left corner of the slide and the Z coordinate represents the position of the Robotic Arm when the Pin barely makes contact with the slide Please refer to 1 10 to see the slide location on the instrument Note There should be only one Pin in the Pin Holder while working in the Slide Spotting mode The Z coordinate should be recorded independently The procedure is the following Step 1 Select the Pre spotting Slide Select the Pre spotting Slide options in the Positions section The last calibrated X Y Z coordinates will be shown in the Calibrated Pos Parameters section and the cu
102. slide Please refer to section 7 6 to 1 know more about 1 Starting at Dispensing Plate Count the Advanced Option Advanced Slide Option 8 7 Array Definition Click the Next button on the Plate page or click the Array button on the array left Task Panel to turn to the Array Definition page CapitalBio Corporation 75 PersonalArrayer 16 Chapter 8 Array First Orray Position Spot Distance micron Spot Count per Channel Max Spot Count Replicate per Sample Multi Array Array Separation Well Count Array Count Max Array Count Array Replication Pre Dispensing be Dipeneng cunt o OOOOOOOO Pre dispensing Plate Dispensing gt Direction Y Direction e m fa DOC Q 2 Q Q Q 2 Q O HI LLL X Direction Y Direction T T H je LLV LLOLL 00 LLL 00 LLL LLK LLL LL Timelmicrosecond lt BackiB N etn 3 In this page users can customize the numbers of arrays that will be printed on the plate how many spots will be in an array and how the arrays and spots are arranged Users can preview the arrangement on a virtual plate in the box on the right In the Plate Dispensing mode each array will occupy a well on the plate First Array Specify which well on the plate the first array will be located in The first array Position in a block of arrays is defined as the top left corner of the block
103. stall and use only one copy of this System on a single computer 2 Make only one copy of this System in a computer readable format for the purpose of making a copy or a managing file on a single computer 3 You can only use this System in a multi user environment or a network system under one of the following conditions It is authorized by this Agreement to be used in a multi user environment or a network system or you have purchased the user license for every related computer License Restrictions 1 You will not assign the license of this System to others 2 You will not conduct any reverse engineering decompiling or disassembling of this System 3 You will not copy or assign this System or any portion of this System 4 This System is licensed as a whole You will not disassemble this System and use its parts and components on more than one computer 5 This Agreement shall not grant you any legal rights relating to any trademarks or service trademarks of CapitalBio 6 You will not rent lease or lend this System to anyone Copyrights All copyrights of this System including but not limited to the copyrights of any photographs pictures cartoons videos recordings music words additional programs printed materials and any copies of this System are exclusively owned by CapitalBio and except for the limited license to use this System granted to you CapitalBio reserves all rights titles and interests in and to this Syste
104. structed below Input Feature Size in um in the text box Feature Size is the expected diameter of the spot on the slides Click the Save GAL button to pop up a dialog to specify the path to save the GAL file Step Step 2 5 9 Cleaning Protocol Click the Next button on the Sample Sequence page or click Lad Clean the Clean button on the left Task Panel to turn to Cleaning Protocol page A Cleaning Protocol can consist of three kinds of operations Rinse Sonicate and Dry A typical Cleaning Protocol has four steps Rinse Sonicate Rinse Dry The number of cycles of this iteration 1s dependent on the sample characteristics Samples with high viscosity require more cycles and an elongated time span It is recommended to optimize the cleaning protocol to save time by conducting a remnant fluorescence test prior to full state usage The procedure to set up a cleaning protocol is described below Select the operation by checking the box in front of the Rinse label and Step 1 click the spin button on the right hand side to specify how long the rinse step will take Click the Add gt gt button to append the cleaning operation list in the right list Step 2 box with the selected operations on the left Step 3 Repeat step 1 and 2 to complete the protocol After you complete the protocol you can make use of the tools provided to Delete Copy Paste Move Up and Move Down a specific entry or delete all entries The user c
105. te exhaust target plate sample plate pre dispense and pre spotting slide The Options available in Positions depends upon working mode as illustrated below Slide Spotting mode Options of Positions ls Rinse C tst Slide T A24 Well Sample L Dry t Sonicate if Peristaltic Slide Dispensing mode Options of Positions Rinse a i Is sige A24 Well Sample T System Liquid Pre dispense Exhaust Led Peristaltic Plate Spotting mode Options of Positions Rinse Hi Well Target A24 Well Sample C Sonicate C Pre spotting Sh Lo Penstaltic Plate Dispensing mode Options of Positions C A24 Well Sample Jogging section contains the following Ul elements X Step Y Step CapitalBio Corporation Dry System Liquid j Pre dispense arna gt Exhaust P i a Peristaltic The distance travelled by the Spotting Module or Dispensing Module along the X the Y or the Z axes per step The maximum _ 28 PersonalArrayer 16 Chapter 4 Configuration Z Step step distance is 50mm for the X axis 40mm for the Y axis and 10mm for the Z axis X Left Click the button to move the Spotting Module or the Dispensing X Right Module along the X axis a step per click Y Forward Click the button to move the Spotting Module or the Dispensing Y Backward Module along the Y axis a step per click Z Up Click the button to
106. th to be dried completely Step 4 Save the calibrated position Specify the X Y Z coordinates to be saved in the check boxes within the Current Pos Parameters section Click the Save button and then confirm to use the current position as the new calibrated position The Spotting Module or the Dispensing Module will move up to the home position along the Z axis 4 2 3 Sonicate Position Calibration The Sonicate Position is where the Sonicator Bath is located It is necessary to calibrate the Sonicate Position to ensure that all 4 Pins on the Pin Holder or the Nozzle can descend into the bath Note The Sonicate Position applies to the Spotting mode In the Dispensing mode the dispenser uptakes the System Liquid from the bath but the Nozzle does not require sonication and the bath position is referred as the System Liquid reservoir position Please refer to section 1 10 to see the bath location on the instrument CapitalBio Corporation 30 PersonalArrayer 16 Chapter 4 Configuration The procedure is the following Step 1 Select Sonicate or System Liquid Select the Sonicate in Spotting mode or the System Liquid in Dispensing mode option in the Positions section The X Y Z coordinates that were last calibrated will be shown in the Calibrated Pos Parameters section and the current X Y Z coordinates of the Spotting module or the Dispensing module will be shown in the Current Pos Parameters section Step
107. the Humidifier remove it from the instrument and check the water level If it is too low please replenish it with deionized water If the program is supposed to run for a long time please check the Humidifier water level at regular intervals Please clean the Humidifier regularly Empty the water from the Humidifier if it is supposed to be out of use for a long time 10 8 Replace Pressure Supply An independent pneumatic pressure source is required for PersonalArrayer 16 under Dispensing working mode The source could be either purified compressed air nitrogen cylinder or purified air compressor The compression resistance of the cylinder should be no less than 14 MPa and inner volume of the bottle should be no less that 8L Before any printing job please check if there is sufficient air nitrogen in the cylinder If not please replenish the cylinder 10 9 Sonicator Bath If the instrument is out of use for two days or longer the Sonicator Bath should be cleaned and the liquid replaced before reuse Step 1 Remove the fluid within the Sonicator Bath with the syringe CapitalBio Corporation 84 PersonalArrayer 16 Chapter 10 Routine Maintenance Step 2 Clean the Sonicator Bath with an alcohol drenched cotton swab Step 3 Fill the Sonicator Bath again 10 10 Fluid Lines The fluid lines should be cleaned before use Step 1 Empty the Wash Buffer Bucket and Waste Bucket Step 2 Fill the Wash Buffer Bucket with fresh
108. tion samples should comply with the following requirements e All of the samples and buffer must be water soluble to ensure that they can be rinsed out completely with the distilled water No corrosive components should be present in the sample The pre treatment procedures such as filtration and purification are indispensable to eliminate large particles in the sample and to avoid high viscosity or clotting The viscosity of the sample solution should be at a low or moderate level to avoid undesirable consequence such as a jammed Nozzle blocked Pin and cross contamination due to incomplete cleaning A level of viscosity lower than 40 glycerol is recommended O For protein the concentration should not be higher than 5mg mL Note Prior to application of a novel sample and buffer system exploratory tests for the better printing or dispensing conditions are compulsory The sample buffer system Pin type slide surface modification process Sample aspiration time Delay time Cleaning Protocol Max spot count per uptake should all be considered for optimization System Cleaning When a novel sample and buffer system are about to be applied exploratory tests for the most effective cleaning protocol are compulsory It is recommended to use fluorescent labeled reagent in such experiments to evaluate the effectiveness of the cleaning procedures When Dispensing the pins should be passed through no less than 2 cleaning cycles pr
109. to the home position along the Z axis 4 3 Dispense Parameters Setting The Dispense dialogue page is available in the Dispensing mode to control pneumatic components and procedures These parameters have already been calibrated by the manufacturer The dialogue page consists of two sections Clean and Dispense as illustrated below CapitalBio Corporation 35 PersonalArrayer 16 Chapter 4 System Configuration Position Calibration Dispense Misc Clean Aspiration pressure kPa 10 00 Dispense Dispense pressure kPa 120 00 System Fluid 2 00 Ratio of Dispense time to G 0 66 Aspiration time Aspiration time s 3 00 Exhaust time s 3 00 Drying time s 1 00 Open Backup The parameters are listed below Clean aspiration time s pressure kPa Air aspiration time s 0 00 Sample aspiration time 0 50 s Dispense pressure kPa 6 00 Drying time s 1 00 Configuration Aspiration pressure kPa 1 10 00 Air aspiration 10 00 The Clean section consists of pressure and time specifications for cleaning procedures The Dispense section consists of pressure and time specifications for the dispensing and Set to Default sample uptake procedures Aspiration pressure Cancel Refers to the pressure applied to take up washing buffer or water in kPa Dispense pressure Refers to the pressure applied to exhaust the washing buffer or water through the nozzl
110. ts printed by the same Pin within an array It must not exceed P the Max Spot Count Max Spot The maximum number of spots is mainly dependent upon the dimensions Count of Printable Area and Spot Distance Refers to how many replicates are required for a single sample It is not Replicate s i supposed to be greater than the product of the values of Spot Count per Pin per Sample l along X axis and Y axis Array l l Define the number of blank wells between two neighboring printed wells Separation Array Refers to the number of arrays arranged on the plate along each axis It must Count not exceed the Max Array Count Max Array Itis determined by Array Separation First Array Position and the number Count of rows and columns on the plate Array o Indicates whether the arrays share the same sample sequence Replication Pre spotting Count Pre spotting Distance can be set on this page Please refer to section 5 7 for more details CapitalBio Corporation 69 PersonalArrayer 16 Chapter 7 Plate Spotting 7 8 Sample Sequence Click the Next button on the Array Definition page or click the Sample nim button on the left Task Panel to turn to Sample Sequence page A graphical interface simulating a 384 well plate is presented to set up Sample Sequence for sample uptake Please refer to section 5 8 for more details 7 9 Cleaning Protocol Click the Next button on the Sample Sequence page or click YY Clean the Clean button
111. ts printed by the same pin channel within an Array The count should not P be greater than the Max Spot Count The maximum number of spots is mainly dependent upon the dimensions of printable area and the Spot Distance The upper limit of the spot count printed by the same Pin within an Array If Max Spot f l i Count there is only one Pin on the Pin Holder the Max Spot Count is determined by the Spot Distance by PX PY If there is more than one Pin the Max Spot Count is determined by the Spot Distance and by the distance between the Pins f Refers to how many replicates are required for a single sample It should not be Replicate s greater than the product of the values of the Spot Count per Pin along the X per Sample l l axis and the Y axis Array The distance between the edges of two neighboring Arrays sub arrays It Separation should not be less than the Spot Distance Array Refers to how many Arrays sub arrays will be arranged on the slide along Count each axis It should not be greater than the Max Array Count Max Array It is determined by Array Separation the size of the array and the printable Count area A n Indicates whether the arrays share the same sample sequence Replication Pre spotting Count CapitalBio Corporation The number of Pre spotting spots per sample ranges from 0 500 Pre spotting is necessary to ensure the uniformity of spots on the slide by 45 PersonalArrayer 16 Chapter 5 Sli
112. ve it Failed to open protocol CapitalBio Corporation 89 PersonalArrayer 16 a nog pe E cd Pa i E Egte IA A TP E eta Ba e eiA Te a k KL 22 Bs EY Gorporation CapitalBio Corporation 18 Life Science Parkway Changping District Beijing 102206 China Tel 86 10 80725793 Fax 86 10 80726782 Email techsupport capitalbio com globalsales capitalbio com http www capitalbio com
113. w many pre spotting slides will be needed The Plate Deck can accommodate up to two 96 well plates and one pre spotting slide Starting at Spotting Plate Count Pre spotting Slide Count 1 Advanced Slide Option CapitalBio Corporation 67 PersonalArrayer 16 Chapter 7 Spotting Well Plate Fre 5 potting Slide Well Geometryt mr Circle Diameter m TE Printable Breat rmrmi Height 3 0205 Width Rectangle Height Width 3 0205 Plate Spotting Click the Advanced Option button on the Plate page to bring up the Plate Advanced Option dialog There are two pages Spotting Well Plate page and Pre spotting Slide page On the Spotting Well Plate page you can decide the Well Geometry to define whether it is round or square and the diameter length or width You can also review the Printable Area in each well described by the length and width dimension Spotting Well Plate Pre Spotting Slide Pre spotting Slide unit mern LN 25 000 oy Z DUDU Px 1 000 7 7 Array Definition rray CapitalBio Corporation IK oy PY Min Margin 5 000 3 000 0 000 1 000 On the Pre spotting Slide page you can decide the Printable Area of the Pre spotting slide Please refer to section 5 6 to learn more Click the Next button on the Plate page or click the Array button on the left Task Panel to turn to the Array Definition page 68 Perso
114. wizard you can always click the Back button to go back to a previous step and make any necessary changes or click the Cancel button to exit the wizard 2 5 Uninstall the Software Like any other Windows application software the PersonalArrayer 16 application software can be uninstalled from the Control Panel Follow these steps to uninstall click on the Add Remove Programs item find PersonalArrayer 16 in the program list choose Change Remove and confirm when notified The program should now be removed CapitalBio Corporation 22 PersonalArrayer 16 Chapter 3 Software Tutorial Chapter 3 Software Tutorial 3 1 Overview In this chapter we will guide you to spot or dispense a microarray on substrates such as slides This way you can quickly grasp the basic skills to use the software and accomplish basic Spotting Dispensing tasks It is mandatory to check the configuration parameters particularly to perform Position Calibration to ensure the system functions correctly when any of the following occur a new system is installed the system is moved or if changes are made to the hardware or software 3 2 Getting Started 3 2 1 Launch the System Step Power on the computer Step 2 Use the USB cable to connect the instrument and the computer power on the instrument Step 3 Select Programs gt CapitalBio gt PersonalArray16 gt PersonalArray16 from Start Menu Step 4 Input correct user n
115. you proceed 5 4 1 Cleaning Operations For the cleaning operations users can undertake following actions Rinse Pin Rinse Dry Pin Dry Sonicate and Pin Sonicate Users may execute each command independently The sections below describe the actions necessary to start and stop each command gt es Idle Rinse Pin Rinse gt gt Idle Sonicate Pin Sonicate 5 4 1 1 Rinse Click the Rinse button and the water in the Rinse Basin will begin to 9 Rinse flow Meanwhile the Rinse Indicator will be illuminated O Rinse Click the Rinse button again to exit the current action The Rinse Indicator will turn off Please ensure that there is sufficient water in the Rinse Basin for the following steps CapitalBio Corporation 40 PersonalArrayer 16 Chapter 5 5 4 1 2 Pin Rinse ue Pin Rinse Slide Spotting Click the Pin Rinse button the water in the Rinse Basin will begin to flow and the Robotic Arm will move to dip the Pin into the basin Meanwhile the Rinse Indicator will be illuminated LJ Pin Rinse 5 4 1 3 Dry dd Dry Click the Pin Rinse button again to exit the current action The Robotic Arm will lift up the Pin out of the basin The Rinse Indicator will turn off Click the Dry button and the vacuum pump will start to work Meanwhile the Dry Indicator will be illuminated Y Dry 5 4 1 4 Pin Dry Click the Dry button again to exit the current action The Dry Indicator wi

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