ABI Prism® 7900HT Sequence Detection System ... - OpenWetWare

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To define the positions of the remaining stacks: (continued) Step Action 8 Using the Vertical Positioning commands, raise and lower plate handler arm several times to check the alignment. 9 Click Rotary Offset, andclickYes. The software records the rotary position for the Zymark position 5 (input stack 2). 10 Repeat steps 1–8 for input stacks 3 and 4 to define Rotary Offset values for the remaining positions 6 and 7: Zymark position 7 (input stack 4) Zymark position 6 (input stack 3) 11 Exit the Zymark Twister Software. a. Click Main Menu. The software displays the main menu. b. Click Exit. The software closes. 12 Note A bug in the Zymark Twister Software can cause portions of the program to persist in memory even after the software has been closed. Because the Zymark Twister Software conflicts with the SDS software, these residual elements must be closed within the Windows Task Manager before continuing. Confirm that the Zymark Twister Software has closed by viewing the Task Manager. a. Press the Ctrl + Alt + Del keys in unison. The Windows Security dialog box appears. b. Click Task Manager. The Task Manager dialog box appears. c. Confirm that the Twister software has closed by looking for the Twister software entry in the Task list. If the software is still running, click the software entry and click End Task to exit the software. d. From the File menu, select Exit to quit the Task Manager. 13 Replace the covers for the fixed-position bar code reader and the underlying platform (removed in step 1 on page 7-32). GR2009 Fixed-position bar code reader and underlying platform covers System Maintenance 7-39
Aligning the Fixed-Position Bar Code Reader Description The fixed-position bar code reader must be set so that it automatically scans the plate’s bar code as the plate is placed into the instrument tray by the plate handler. Preparing the Instrument for the Alignment Positioning the Fixed-Position Bar Code Reader 7-40 System Maintenance To move the instrument tray to the Out position: Step Action 1 Remove the cover for the fixed-position bar code reader. 2 Turn on the computer. 3 Launch the Automation Controller Software. 4 Click Open/Close ( ). The 7900HT instrument moves the instrument tray to the out position, perpendicular to the instrument. 5 From the File menu, select Exit. The software quits the Automation Controller Software. IMPORTANT The instrument tray must be in the OUT position to align the bar code reader. To position the fixed-position bar code reader: Step Action 1 Place a plate with bar code onto the instrument tray. GR2009 Fixed-position bar code reader cover IMPORTANT Orient the plate so that well A1 aligns to the A1 position of the instrument tray and that the bar code faces the fixed-position bar code reader. 2 Select Start > Programs > PSC Laser Data > LDHOST. The LDHOST software launches and displays the LDHOST window. GR2018 Well position A1 Bar code
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ABI PRISM ® 7900HT Sequence Detect
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© Copyright 2001, Applied Biosyste
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iv Section:PlateDocumentSetup......
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vi A Theory of Operation Fluorescen
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Attention Words and Warning Labels
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About Waste Profiles A waste profil
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Safe Instrument Use Before Operatin
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Product Overview 2 In This Chapter
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Section: Getting to Know the Hardwa
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Interchangeable Thermal Cycler Bloc
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Computer Description The computer c
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Zymark Twister Microplate Handler D
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Instrument Connections Electrical C
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Section: Getting to Know the Softwa
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Managing Sequence Detection System
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Getting Started 3 In This Chapter T
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Using the SDS Software Online Help
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Turning on the ABI PRISM 7900HT Seq
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Using the SDS Software Workspace La
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Using the General Toolbar Using the
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Basic Software Skills Tutorial Abou
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Exercise 3: Opening a Plate Documen
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Lesson 2: Viewing and Resizing Pane
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Exercise 2: Selecting Multiple Well
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Lesson 4: Using the Hand-Held Bar C
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Using SDS Plate Documents Using Mul
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Run Setup and Basic Operation 4 In
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Setup Checklists Experiments/Runs P
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Section: Plate Document Setup In Th
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Step 2 - Applying Detectors and Mar
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Creating an Allelic Discrimination
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Step 3 - Configuring the Plate Docu
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Step 4 - Programming the Plate Docu
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To create a method for the absolute
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Step 5 - Saving the Plate Document
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Step 7 - Applying Sample and Plate
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Section: Running an Individual Plat
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Preparing and Running a Single Plat
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Operating the 7900HT Instrument Usi
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After the Run Analyzing the Run Dat
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Section: Running Multiple Plates Us
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Adding a Plate Document to the Plat
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To create plate documents from a te
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Adding Plates to the Plate Queue Re
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Loading Plates To load plates onto
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End-Point Analysis 5 In This Chapte
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Section: Allelic Discrimination In
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Algorithmic Manipulation of Raw All
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Before You Begin Using SDS Online H
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Analyzing a Completed Allelic Discr
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Calling Allele Types To call allele
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Scrutinizing the Allele Calls To an
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After the Analysis Changing the Pla
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Real-Time Runs on the 7900HT Instru
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Overview About Absolute Quantificat
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Before You Begin Using SDS Online H
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Analyzing the Run Data Configuring
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Setting the Baseline and Threshold
Page 119 and 120: Eliminating Outliers For any PCR, e
Page 121 and 122: Viewing the Standard Curve 6-14 Rea
Page 123 and 124: 6-16 Real-Time Analysis
Page 125 and 126: Overview About Dissociation Curve A
Page 127 and 128: Analysis Checklist WhereYouArein th
Page 129 and 130: Determining T m Values for the Anal
Page 131 and 132: After the Analysis Changing the Pla
Page 133 and 134: Recommended Maintenance Schedule Ma
Page 135 and 136: Replacing the Sample Block When to
Page 137 and 138: 7-6 System Maintenance To remove th
Page 139 and 140: 7-8 System Maintenance To replace t
Page 141 and 142: 7-10 System Maintenance To replace
Page 143 and 144: Cleaning the Sample Block Wells 7-1
Page 145 and 146: Prepare a Background Plate Document
Page 147 and 148: Extracting the Background 7-16 Syst
Page 149 and 150: Materials Required The following ma
Page 151 and 152: Extracting Pure Dye Information fro
Page 153 and 154: Constructing a Custom Pure Dye Plat
Page 155 and 156: Verifying Instrument Performance Us
Page 157 and 158: Preparing and Running an RNase P Pl
Page 159 and 160: Adjusting the Sensitivity of the Pl
Page 161 and 162: Testing the Adjustment 7-30 System
Page 163 and 164: Aligning the Plate Handler When to
Page 165 and 166: 7-34 System Maintenance To align th
Page 167 and 168: Re-checking the Input Stack 1 7-36
Page 169: Defining the Positions of the Remai
Page 173 and 174: 7-42 System Maintenance To position
Page 175 and 176: 7-44 System Maintenance
Page 177 and 178: General Computer Maintenance Mainte
Page 179 and 180: Maintaining the SDS software Admini
Page 181 and 182: Troubleshooting Table 8-2 Troublesh
Page 183 and 184: Low Precision or Irreproducibility
Page 185 and 186: Writing on the Reaction Plates Fluo
Page 187 and 188: Background Runs Background Troubles
Page 189 and 190: Pure Dye Runs Pure Dye Troubleshoot
Page 191 and 192: 8-12 Troubleshooting Troubleshootin
Page 193 and 194: Software and 7900HT Instrument Trou
Page 195 and 196: 8-16 Troubleshooting Troubleshootin
Page 198: User Bulletins 9 9 About This Chapt
Page 201 and 202: Fluorescent-Based Chemistries Funda
Page 203 and 204: Fluorescence Detection and Data Col
Page 205 and 206: Normalization of Reporter Signals A
Page 207 and 208: Determining Initial Template Concen
Page 209 and 210: Calculating Threshold Cycles A-10 T
Page 212 and 213: Importing and Exporting Plate Docum
Page 214 and 215: Configuring the Setup Table File wi
Page 216 and 217: About the Setup Table File Format S
Page 218 and 219: Setup Table Elements (continued) Nu
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Exporting Plate Document Data Expor
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Designing TaqMan Assays C In This A
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Design Probes and Primers The follo
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Design Tips for Allelic Discriminat
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Kits, Reagents and Consumables D In
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Consumables and Disposables The ABI
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TaqMan Pre-Developed Assays and Rea
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Contacting Technical Support F Serv
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G-2 Limited Warranty Statement No a
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A(continued) Automation Controller
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I(continued) installing plate adapt
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Q quantifying probes and primers C-
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Headquarters 850 Lincoln Centre Dri
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