Page 1 ™ Applied Biosystems 3500/3500xL Genetic Analyzer USER GUIDE with 3500 Series Data Collection Software 3.1 Catalog Numbers 4405186, 4405187 Publication Number 100031809 Revision C For Research Use Only. Not for use in diagnostic procedures.
Page 2 New information for version 3.1 software: Change buffer and polymer limits to 14 days. Updates: Information for 96-sample polymer pouches. Instruction to ensure CBC septum is properly seated. New run modules. Corrections: Remove sample limits on buffer. Correct part numbers for 3500/3500xL Sequencing Standards, BigDye ™...
Page 3: Table Of Contents
Important notice regarding use of consumables that exceed supported limits ..22 Overview of the 3500 Series Data Collection Software 3.1 ......23 About the software .
Page 4 Step one: Start the Server Monitor ......... . . 30 Step two: Start the 3500 Series Data Collection Software 3.1 ....31 Step three: Log in .
Page 5 Review results for the currently running sequencing plate ......83 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 6 Modify fragment analysis or HID data ..........102 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 7 Perform the fragment/HID install check ........133 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 8 ........... . . 160 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 9 Generate audit reports ........... . 204 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 10 Reactivate the instrument ..........242 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 11 Reset the instrument ............280 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 12 When to use the normalization feature ......... . . 300 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 13 Index ..............313 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 14: Chapter 1 Instrument And Software Description
Instrument consumables handling, usage limits, and expiration ... . 19 ■ Overview of the 3500 Series Data Collection Software 3.1 ....23 Instrument and software description...
Page 15: Precautions For Use
Figure 1 Instrument interior Detection cell heater block Polymer delivery pump (PDP) Anode buffer container (ABC) Polymer or conditioning pouch Cathode buffer container (CBC) Oven door Capillary array Oven condensation reservoir Autosampler 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 16: Instrument Parts And Functions
RFID tags are read and written in response to a user action (for example, running a wizard or starting a run). All dashboard values are updated when RFID tags are read and written. The days on Instrument is also updated automatically every 6 minutes. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 17: Instrument Front Panel Indicators
IMPORTANT! Do not rename the computer after the 3500 Series Data Collection Software 3.1 is installed. The instrument computer has been assigned a unique name. Changing the name may cause the 3500 Series Data Collection Software 3.1 to malfunction. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 18: Instrument Firmware
4 different dyes are used to determine the 4 bases A, G, C and T. For fragment analysis applications, up to 6 dyes can be used in a single run for higher throughput. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 19: Results
The 1X running buffer has been qualified to ship at ambient conditions. For a description of the 4408256 Cathode Buffer Container (CBC) 1X running qualification, go to buffer, 4 containers http://find.thermofisher.com/ce/ambientbuffers/ email?CID=fl-we18868. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 20: Polymer
> 25°C, the supported limit is 7 days. For the POP-6 ™ Polymers (Cat. Nos. A26071, 4393717, and 4393712), the on-instrument supported limit is 14 days when the instrument operating temperature is 15–30°C. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 21: Conditioning Reagent
WARNING! SHARP The load-end of the capillary array has small, blunt ends that can lead to piercing injury. Cat. No. Description Storage 4404685 8-Capillary, 50 cm Room temperature 4404689 24-Capillary, 50 cm 4404683 8-Capillary, 36 cm 4404687 24-Capillary, 36 cm 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 22: Hi-Di ™ Formamide
Life Technologies instructions for the instrument system, software, or accessories. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 23: Overview Of The 3500 Series Data Collection Software 3.1
Chapter 1 Instrument and software description Overview of the 3500 Series Data Collection Software 3.1 Please see your specific service contract or limited product warranty for exact language regarding coverage and ask your Life Technologies representative if you have further questions.
Page 24: Workflow
Chapter 1 Instrument and software description Overview of the 3500 Series Data Collection Software 3.1 The Dashboard gives you quick access to the information and tasks you need to set up and run: • Workflow, Maintenance, and Library tabs—Advances to the screens to set up, load, run, and review plates, maintenance wizards, and library items.
Page 25: Maintenance Workflow
Chapter 1 Instrument and software description Overview of the 3500 Series Data Collection Software 3.1 Maintenance Select Maintenance in the menu bar to access the Maintenance workflow. workflow The Maintenance workflow contains the screens where you calibrate, run install checks, run maintenance procedures, and access records about instrument maintenance and service.
Page 26: Sae Menu
Chapter 1 Instrument and software description Overview of the 3500 Series Data Collection Software 3.1 SAE menu This option is available if your system includes a license for the Security, Audit, and E-Signature module. Select SAE in the menu bar to access: •...
Page 27: Preferences Menu
For details about tasks and other information, refer to the chapters in this user guide. Use the software You can install the 3500 Series Data Collection Software 3.1 on a computer that is not connected to an instrument. You can use this stand-alone version of the software to: without an instrument •...
Page 28: Chapter 2 Start The System
When the green front panel indicator stops blinking, log in to Windows operating system, then start the software (see “Start the software“ on page 30) “Check calendar reminders“ on page 32 “Check consumables status“ on page 33 “Replenish consumables“ on page 35 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 29: Start The Computer And Instrument
CAUTION! Do not unpack or plug in any components until a service representative has configured the system for the proper operating voltage. IMPORTANT! Do not rename the computer after the 3500 Series Data Collection Software 3.1 is installed. The instrument computer has been assigned a unique name.
Page 30: Start The Software
It takes ~1 minute for the Server Monitor to start up. When the Server Monitor icon is displayed, go to “Step two: Start the 3500 Series Data Collection Software 3.1“ on page 31 below. IMPORTANT! If the Server Monitor icon does not change to , you cannot start the software.
Page 31: Step Two: Start The 3500 Series Data Collection Software 3.1
Step two: Start the Select Start4Programs4Applied Biosystems4350043500. 3500 Series Data The 3500 Series Data Collection Software 3.1 splash screen is displayed for a few Collection seconds, then the 3500 Series Data Collection Software 3.1 Login dialog box opens. Software 3.1...
Page 32: Check System Status In The Dashboard
Notifications Log (for more information, see “Review the Notifications Log“ on page 228. 3. Perform any daily, monthly, or quarterly tasks that are not listed in the Calendar Reminders pane (see “Maintenance schedule“ on page 223). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 33: Check Consumables Status
The consumable also displays in red in the Consumables pane. IMPORTANT! We recommend that you add a calendar reminder to the schedule for polymer and buffer replacement. Set the notification to display 2 days before the polymer should be replaced. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 34: How The Polymer Sample And Injection Counters Calculate Usage
The meniscus must line up at or above the fill line. levels Ensure that the septa on the CBC are properly seated. IMPORTANT! Replace the buffer if the buffer level is too low. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 35: Replenish Consumables
When you install the CBC buffer septa, press firmly to seat the septa. installation of CBC septa IMPORTANT! Look at the CBC from the side and ensure that there is no gap between the container and the lip of the septum. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 36: Set Preferences (Optional)
• Reports Settings • Run Setup • Sequencing Settings (review and report settings) • Warning dialogs Note: Users can also save user preferences while viewing tables. See “Customize a table“ on page 76. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 37: System Preferences
You can disable filters in each location to display all items. Plate setup Default settings for plate name. Reports Settings Default font and text size and custom logo in reports. Note: You can override this setting in each report view. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 38 • Plate report—Trace Score Set colors and ranges: a. Click a color bar to select a new color. b. Place the mouse pointer over a slider, then drag to set a new range. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 39 • Display well image by—Specify the thumbnail option for Plate Reports: Wider thumbnail without file name or Smaller thumbnail without file name. Warning Dialogs Suppress warning messages for deleting an injection or exporting a library item. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 40: Chapter 3 Set Up And Run
More features in Monitor Run ......... . 80 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 41: Setup Workflow
4. Check the pump assembly for bubbles and run the Remove Bubble wizard if needed (see “Remove bubbles from the polymer pump“ on page 237). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 42: Create Or Import A Plate
For more information, see “Create a plate from a template“ on page 42. 1. In the Dashboard, click Create Plate From Template to display the Open Plate Template from Library dialog box. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 43 4. (Optional) In the bottom section of the screen, specify auto-analysis settings for the plate. Refer to the instructions provided with the secondary analysis software. 5. Click Save. 6. Click Assign Plate Contents, then go to “Assign plate contents“ on page 44. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 44: Import A Plate
Import a plate 1. Do either of the following: • Create a plate on another 3500 Series Data Collection Software 3.1 computer, then export (see “Import and export a plate“ on page 79). • Create a plate import file (see “Create a plate import file“ on page 78.
Page 45: Access The Assign Plate Contents Screen
• The Dashboard by clicking the Workflow tab, then selecting Assign Plate Contents in the navigation pane. 2. Click Show In Wells to specify the attributes to display in wells. Figure 4 shows the Plate View of the Assign Plate Contents screen. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 46 Chapter 3 Set up and run Assign plate contents Figure 4 Assign plate Contents Show well attributes Name samples Assign assays, file name conventions, and results groups Assign sample types and user-defined fields Link plate for run 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 47: Name Samples And Assign Sample Types In The Plate View
Note: To use Fill Series, type a number as the last character of the named well. The number will increment for each well in the series. Note: You can copy and paste sample names instead of using fill commands. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 48 Microsoft ™ Word ™ , which may include invisible, non-ASCII characters. Non- ASCII characters in plate or sample information may cause a run to stop or may prevent a run from starting. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 49: Assign Assay, File Name Convention, And Results Group In The Plate View
2. Select the checkbox next to the assay name to assign the assay to the selected wells. 3. Repeat for file name conventions and results group. 4. Select Save Plate. 5. Go to “Print the plate layout“ on page 50. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 50: How File Location In File Name Conventions And Results Groups Work
Writer as the printer. 4. Close the report. 5. Go to “Prepare and load sample plates“ on page 50. Prepare and load sample plates IMPORTANT! Do not use warped or damaged plates. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 51: Capillary-To-Plate Mapping
However, during internal HID validation studies, verify the required allelic ladder injection frequency to ensure accurate genotyping of all samples in your laboratory environment. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 52: Results Group For One Allelic Ladder Per Run Folder
4. Store the plate on ice and protected from light until you prepare the plate assembly and load the plate in the instrument. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 53: Prepare The Plate Assembly
5. If the contents of any well contain bubbles or are not located at the bottom of the well, briefly centrifuge the plate, remove the plate from the centrifuge, and verify that each sample is positioned correctly in the bottom of its well. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 54 See Appendix D, “Catalog numbers“ for plate assembly specifications and catalog numbers. Figure 5 8-strip standard tube assembly Plate retainer Septa Retainer 8-strip tubes 96-well tray Plate base 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 55 7. If the reagents of any well contain bubbles or are not located at the bottom of the well, briefly centrifuge the plate, remove the plate from the centrifuge, and verify that each sample is positioned correctly in the bottom of its well. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 56: Load The Plate In The Instrument
2. Place the plate in the autosampler with the labels facing you (or the instrument door) and the notched corner of the plate in the notched corner of the autosampler. 3. Close the instrument door to initialize the instrument. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 57: Link The Plate
1. In the Assign Plates for Run screen, click Link Plate for Run. Note: By default, plate A position is selected. 2. Go to “Load plates for run and create the injection list“ on page 59. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 58: Quick Start A Run
3. Click Start Run from the Load Plates for Run screen. Note: If an install check for the run application type (Sequencing or Fragment) has not been performed, a message is displayed and the run does not start. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 59: Load Plates For Run And Create The Injection List
For example, if you link two plates, then start the run, both plates and any duplicate injections or re-injections are part of the same instrument run. An injection is an instance of 8 or 24 samples (depending on instrument configuration) processed simultaneously under the same conditions. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 60 4. If needed, click Unlink, then follow the steps in “Link a plate (if a plate is not linked)“ on page 61. 5. As needed, click Switch Plates ( ) to assign the plate to the other position in the autosampler. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 61: Link A Plate (If A Plate Is Not Linked)
If you access the Load Plates for Run screen from the navigation pane, a plate may not be linked (indicated by the active Link Plate button). plate is not linked) To link a plate: 1. Click Link Plate to display the Select Plate from Library dialog box. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 62: Link A Plate From The Recent Plates Or Recent Runs Tab
• The Load Plates for Run screen by clicking Create Injection List. • The navigation pane by selecting Preview Run. • The Dashboard by clicking the Workflow tab, then selecting Preview Run in the navigation pane. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 63 Click an injection to select the associated wells in the plate view. IMPORTANT! If the injection list is blank, make sure that you clicked Create Injection List on the Load Plates for Run screen. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 64: Start The Run From Preview Run
Note: If an install check for the run application type (Sequencing or Fragment) has not been performed, a message is displayed and the run does not start. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 65: Monitor The Run
Figure 9 Monitor Run screen 1. Click the Table Settings button, then specify the columns to show or hide in the injection list. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 66 Average QV values that are in the suspect range, and red marks are displayed for wells with Average QV values that are out of range. • Place the mouse pointer over a well to display sample details. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 67: Check Sequence Or Sample Quality And Re-Inject Samples
Note: If the Injection, Analysis, or Flag columns are not displayed, you can click the Table Settings button, then show them in the injection list. Check sequence 1. Expand the Flag pane at the bottom right of the screen. or sample quality 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 68 (red) The Sizing Quality is in the Suspect (fragment) or Fail range. For information, see “Sizecalling protocol— QC settings“ on page 184. IMPORTANT! Normalization is not applied to samples (green, yellow, red) with (red) Sizing Quality. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 69: Re-Inject Samples From The Monitor Run Screen
1. Select the samples in the flag table contain flags (see “Check sequence or sample quality“ on page 67). 2. Click Re-inject. Note: If you are running an HID plate, see “Re-inject HID allelic ladder samples“ on page 71. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 70: If You Select A Protocol Other Than The Original
If the Injection Number attribute is selected for display in the plate view, the number of the original injection and the re-injection are shown. are displayed in the plate view Sample 1 selected for re-injection Re-injection number listed for all samples in the re-injection 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 71: Re-Inject Hid Allelic Ladder Samples
To identify allelic ladder samples for re-injection, include the well position in the allelic ladder sample name when you assign plate contents. 2. Select whether to collect data for the remaining samples in the allelic ladder re- injection. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 72: Review Completed Injections In Review Results
• Terminate injection list—Stops the instrument run. Terminate is active only after you click Pause or Abort. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 73: More Features In Assign Plate Contents
• Select all wells. one time • Select assays, file name conventions, and results group for the plate. • Enter name and select sample type (in the Customize Sample Info pane) for the whole plate. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 74: Customize The Plate View
1. Click Show In Wells to specify the attributes to display in wells. plate view 2. Click Select Wells to select wells with a specific attribute. 3. Click Zoom In, Zoom Out, and Fit as needed. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 75: View The Capillary-To-Plate Map
1. Click Table View. Use the table view 2. Click the Sample Name field, then type a name. 3. 3. Click next to each field, then select a setting. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 76: Sort By One Or Multiple Columns
• Apply—To use the settings for this session only. • Save to Preferences—To save for future use by all users. Preferences are saved for the logged-in user. • Restore Defaults—To restore factory-default settings. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 77: Add Assays, File Name Conventions, And Results Groups To A Plate
Software 3.1. To create a template for importing plate information, set up a plate in the 3500 Series Data Collection Software 3.1, then export it to create a file that contains the correct header and column information for importing: 1.
Page 78: Create A Plate Import File
, which may include invisible, non-ASCII characters. Non- ASCII characters in plate or sample information may cause a run to stop or may prevent a run from starting. 5. Save the plate import file. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 79: Edit A Plate
You can import and export plates from: a plate • Plates library—Plates in .xml format for use on another 3500 instrument. See “Import and export a library entry“ on page 141. • Define plate properties— Plates in .txt, .csv, and .xls format—Files you create that contain plate information in a specific format.
Page 80: Specify The Default Plate Type For The Open Plate Dialog Box
• Click to detach a view and display it in a separate window that you can move around on the screen. To locate a detached view, click the 3500 task bar icon. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 81: Array View
The EPT view (ElectroPhoresis Telemetry) shows instrument data conditions (laser power, temperatures, electrophoresis voltage) as a function of time. In the legend to the right of the EPT view, you can select and deselect the traces to display in the view. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 82: Chapter 4 Review Sequencing Results
Access the View Sequencing Results screen from: • The Monitor Run screen by clicking Review Results. • The navigation pane by selecting View Sequencing Results. • The Dashboard by clicking View Run Results. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 83: Review Results For The Currently Running Sequencing Plate
Note: The basecaller version listed in the basecalling protocol is limited to a 3-digit number. The version listed in sequencing results is a 4-digit number. The fourth digit is an internal number used by the software. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 84: Review Previously Run Sequencing Samples
2. Click the Table Settings button, then specify the columns to show or hide. 3. Double-click column headers to sort columns. Multi-column sorting is supported (see “Sort by one or multiple columns“ on page 76). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 85 100 RFU; PuP=10 5. Review warnings: a. Scroll to the right of the Metric Analysis table to display the Warning column. b. Display the Analysis Status legend. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 86: Review Traces
3. (Optional) Modify trace display: • Use the Tile Viewer options to display up to four traces at a time. • Set trace colors in Preferences (see “Overview“ on page 36). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 87: Display Thumbnails
6. Click the tabs at the bottom of the trace pane for different views of the data. 1. Click the View Thumbnails button to display results as thumbnails. Display Viewing options Peak Place mouse pointer Move slider to thumbnails (analyzed data) in trace to zoom scale vertically 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 88: Understand Quality Values (Qvs)
• Mixed bases have a maximum QV of 20. • Review all mixed base calls. Quality values (QV) and probability of 79.0% 0.10% error (Pe) 32.0% 0.032% 10.0% 0.010% 3.2% 0.0032% 1.0% 0.0010% 0.32% 0.00010% 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 89: Re-Inject Samples From Review Sequencing Results
4. To print the report, click Print, then preview or print. 5. To save the report electronically (.pdf), print the report and select CutePDF Writer as the printer. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 90: Report Options
SeqScape Software 3 (or later), MicroSEQ ™ ID Analysis Software v3.0 (or later), Variant Reporter ™ Software 2 (or later), and Sequence Analysis (SeqA) Software 6 (or later). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 91: Chapter 5 Review Fragment/Hid Analysis Results
“Review sample quality“ on page 94 “Re-inject samples from Review fragment results“ on page 101 “View, print, and save (.pdf) sample quality reports“ on page 101 “Export sizing results“ on page 102 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 92: Access The View Fragment/Hid Results Screen
Access the View Fragment Results screen from: • The Monitor Run screen by clicking Review Results. • The navigation pane by clicking View Fragment Results. • The Dashboard by clicking View Run Results. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 93: Review Results For The Currently Running Fragment/Hid Analysis Plate
Select one or more samples in the samples table to display their data in the plot view and sizing table view. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 94: Review Previously Run Fragment Analysis/Hid Samples
2. Double-click Offscale, Pull-Up (fragment), Broad Peak (HID), and SQ columns to sort suspect and failing flags to the top of the table. Multi-column sorting is supported (see “Sort by one or multiple columns“ on page 76). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 95 No Data—Normalization is enabled, but Sizing Quality is NO—Sample was not collected with a normalization size standard. N/A—Sample was not collected on a 3500 instrument. For more information, see “Review normalized data“ on page 96. Note: If the Sizing Quality is...
Page 96: Review Normalized Data
7. Indicates the normalization state of the sample in the Normalization Limit column in the Samples View. Normalization If normalization is applied in the 3500 Series Data Collection Software 3.1, the calculated Normalization factor is stored with the raw data and is applied to the raw factor in ™...
Page 97: Review Plots
(Plot Settings) in the plot view toolbar. For information on plot settings, click in the plot settings tabs. settings If the button is dimmed, the Plot Settings dialog is open. Click the 3500 task bar icon, then select Plot Settings. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 98: Overlay Samples
Label Peaks. • Select Retain Labels. 3. Click Save to Preferences to save these settings for future use. You can change preferences at any time. 4. Click Apply. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 99: View Thumbnails
Name column header to select the entire column. 2. Click Rename. 3. In the Search field, enter the sample name to change. 4. In the Rename field, enter the new name. 5. Click Search, then click Rename. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 100: Sort By One Or Multiple Columns
(Plot Settings) in the plot view toolbar, then select Show Labels in the Labels tab. Click Save to Preferences to retain this setting. 4. Ensure that all size standard peaks are present and correctly labeled. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 101: Overlay The Sizing Curve
• Plate—One page per plate for all selected samples that shows the well-location thumbnail traces with color-coded headers that reflect sizing quality. Plot zooming is not retained in the report. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 102: Export Sizing Results
To edit, modify, or further analyze fragment analysis or HID data, import the sample data files into a secondary analysis software application such as: • Fragment analysis—GeneMapper ™ Software 5 (or later) ™ • HID—GeneMapper ID-X Software v1.2 (or later) 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 103: Chapter 6 Run Calibrations And Install Checks
Run a fragment/HID install check ........130 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 104: Section 6.1 Run Spatial And Spectral Calibrations
• 24-cap: 3,000 RFU (number of peaks) Individual peak height Peak height 1,000 RFU Uniformity (peak height (standard deviation) similarity) divided by (average peak height) Capillary spacing max. spacing - min. spacing 2 pixels 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 105: Evaluate The Spatial Calibration Profile
If the results do not meet the criteria above, the Accept button is dimmed. Go to “Spatial calibration troubleshooting“ on page 271. IMPORTANT! Do not log off or close the software before clicking Accept Results. Spatial calibration results are not saved until you click Accept Results. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 106: Example Spatial Profiles
2. Enter an export file name. 3. Select the export file type, then click Save. The export file contains the following results: • Capillary Number • Position (pixels) • Spacing • Intensity 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 107: View And Print A Calibration Report
Note: For sequencing applications, you can skip this process, and run the Sequencing install check. If you select Keep Spectral Calibration Data in the Install Check, the software runs a spectral calibration for the dye set during a sequencing check and 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 108: Estimated Run Time
See Appendix D, “Catalog numbers“ for catalog numbers. If peaks are offscale for G5, F, and E5 dye sets, dilute the matrix standard and repeat the calibration. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 109 Columns 1, 3, and 5 in rows A, C, E, G, I, K, M, O 384-well plate Note: 384-well plates are not supported on 8‑capillary instruments. 2. Briefly centrifuge the plate that contains the standards. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 110 2. Place the plate in the autosampler with the labels facing you (or the instrument door) and the notched corner of the plate in the notched corner of the autosampler. 3. Close the instrument door to initialize the instrument. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 111: Perform A Spectral Calibration
3. Select the plate position for the plate loaded in the instrument. Note: You do not create a plate in the software for the calibration. 4. Specify the starting well for the injection position in which you loaded the standard in the plate. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 112 To display the result for each capillary (spectral data, Quality Value, and Condition Number) below the run results table, click a capillary in the table. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 113: Spectral Quality Values And Condition Numbers
The ranges that the software uses to determine if a capillary passes or fails are: Condition Number Dye set Quality Value minimum maximum AnyDye 0.8 (default) 20.0 (default) 0.95 0.95 0.95 0.95 13.5 0.95 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 114: Evaluate The Spectral Calibration Data
• 5-dye: orange-red-yellow-green- blue Extraneous peaks in the raw data None profile (intensity vs scan) Note: The E5 profile may include extraneous peaks outside the matrix peak region, which can be ignored. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 115: What You See During A Spectral Calibration
(or mirror image peaks). While the run is in progress, these pull-down peaks will eventually correct themselves. Once the run completes the electropherogram, the pull-down peaks disappear. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 116: Capillary Information Sharing
Value and Condition Number limits) within the borrowing limits: • 8-capillary instruments – One adjacent-capillary borrowing event allowed • 24-capillary instruments – Up to three adjacent-capillary borrowing events allowed (the number of allowed borrowing events can be decreased in Preferences). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 117 • If all capillaries now pass, the calibration passes. • If after borrowing, >1 or > 3 capillaries from injection 1, 2, or 3 do not pass, the calibration fails. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 118: Example Spectral Calibration Data
Chapter 6 Run calibrations and install checks Run a spectral calibration Example spectral Dye Set E created from Sequencing Standard calibration data Dye Set Z created from Sequencing Standard Dye Set G5 created from Matrix Standard Set DS-33 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 119: Export Spectral Calibration Results
2. (Optional) In the Report screen, click toolbar options to manipulate the report. Place the mouse pointer over an item for a description of the item. 3. To print the report, click Print. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 120: Save Historical Reports (.Pdf) For Record Keeping
View the spectral Only the most recent spectral calibration for each dye set is maintained in the software. calibration history Select History View, then select a dye set to view the associated calibration history. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 121: Section 6.2 Run An Install Check
4. Check the pump assembly for bubbles and run the Remove Bubble wizard if needed (see “Remove bubbles from the polymer pump“ on page 237). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 122 Columns 1, 3, and 5 in rows A, C, E, G, I, K, M, O 384-well plate Note: 384-well plates are not supported on 8‑capillary instruments. 2. Briefly centrifuge the plate that contains the standards. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 123: Perform A Sequencing Install Check
(it can ™ be used for application runs). If your application uses BDTv3.1 with POP-6 polymer, select BDTv.1 for the sequencing install check, then perform a separate 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 124 Note: The spectral calibration record will only be saved if the Keep Spectral Calibration Data option is checked on the screen. If you uncheck the option, create a separate spectral calibration from the Maintenance menu. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 125: What You See During A Sequencing Install Check
IMPORTANT! Do not accept a sequencing installation standard run until you examine the data. What you see The instrument performs one run, then evaluates: during a • Spectral data, if you specified to keep spectral data sequencing install • Sequence data check 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 126: Pass/Fail Criteria For The Optional Spectral Calibration
The number of borrowing events can be decreased (see “System preferences“ on page 37). Thresholds used by the software for pass/fail are listed in the following table: Condition Number Dye set Quality Value minimum maximum 0.95 0.95 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 127: Pass/Fail Criteria For The Sequencing Install Check
Basepair Accuracy calculates the percent of accurate Length Accuracy) basecalls in the known reference sequence within the Read Length of the sequencing install standard. CRL Median and SD Median and standard deviation determined for all capillaries. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 128: Evaluate Sequencing Install Standard Data
4. If the data for the required number of capillaries meets the criteria above (at least 7 capillaries for 8-capillary instruments, at least 22 capillaries for 24-capillary instruments), click Accept Results. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 129: Example Sequencing Install Check Results
IMPORTANT! If you reject results, the spectral calibration is not saved. Example sequencing install check results View previously Select History View, then select an install standard to view the associated install check information. run install standards 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 130: View And Print An Install Check Report
Polymer, 36-cm capillary array)—≤ 30 minutes Prepare for the Before you begin fragment/HID If you have not already done so, perform a spectral calibration (see “Perform a install check spectral calibration“ on page 111). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 131 1, but you can specify the starting well for an injection position. IMPORTANT! You do not create a plate in the software for the install check. 8-capillary A1 through H1 96-well plate 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 132 4. Store the plate on ice until you prepare the plate assembly and load the plate in the instrument. 5. Prepare the plate assembly as described in “Prepare the plate assembly“ on page 53. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 133: Perform The Fragment/Hid Install Check
2. Select the plate type (number of wells). 3. Select the plate position in the instrument. Note: You do not create a plate in the software for the install check. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 134: What You See During A Fragment Install Check
Results for each allele are shown at the bottom of the screen in the Run Information table. Number of peaks per capillary Plot and allele size/height for selected capillary Allele results for all capillaries 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 135: Pass/Fail Criteria For The Fragment/Hid Install Check
If the run is acceptable, the software allows you to deselect capillaries and recalculate results. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 136: Example Fragment Install Standard Results
Run a fragment/HID install check Example fragment install standard results Example HID install standard results View previously Select History View, then select an install standard to view the associated install check information. run install standards 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 137: View And Print An Install Check Report
Only the most recent results are maintained in the software. record keeping 1. Click View Report. 2. Click Print. 3. In the Printer dialog box, select CutePDF Writer as the printer. 4. Specify a name and location for the report. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 138: Chapter 7 Manage Library Resources
– Instrument protocols – Primary analysis protocols—Basecalling (sequencing), sizecalling (fragment analysis), QC (HID analysis) • Items you select when you create instrument sizecalling and QC protocols: – Dye sets – Size standards 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 139: Factory-Provided Template And Locked Items
Chapter 7 Manage library resources General library procedures Factory-provided The 3500 Series Data Collection Software 3.1 libraries include factory-provided items that are optimized for different applications (for example, instrument protocols with template and specific run modules and primary analysis protocols with specific settings). You can locked items use the factory-provided items directly.
Page 140: Create A New Entry From A Factory-Provided Template Or Locked Entry
Note: To edit a plate template, select the template from the main workflow. Go to Define Plate Properties4Open Plate4Edit Existing Template. 1. Select an item, then click Edit. 2. Modify parameters as needed. 3. Click Save. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 141: Import And Export A Library Entry
Chapter 7 Manage library resources General library procedures Import and export To import or export .xml files for use with other 3500 Series Data Collection Software 3.1 instruments: a library entry • Import—Click Import, then select the .xml file to import. If any items in the import file exist in the library, the software displays a message and gives you the option to replace or skip the item.
Page 142: Customize A Table
Appendix B, “Run modules and dye sets“ lists the run time and size or base range collected for each run module. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 143: Create A New Plate
Plates library Create a new plate If you are running a stand-alone version of the 3500 Series Data Collection Software 3.1 (a version that is not installed on the instrument computer), you can create plates, then export them for use on the instrument computer.
Page 144: Define Plate Properties
For information on how changes are tracked if auditing is enabled, see “Audit action“ on page 205. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 145: Create A New Assay
The list of items in the library may be filtered based on the library filtering user preference. Click Disable Filters to show all items in the list. 2. Select an assay. 3. Click Edit. Note: You can also create an assay from the Assign Plate Contents screen. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 146: Assay Settings
Prevents the item from being edited. Color Color code for the assay when it is displayed in the Assign Plate Contents screen (if Assay Color is selected for Show In Wells). Application Type Sequencing or Fragment. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 147: File Name Conventions Library
See “Set preferences (optional)“ on page 36.) • Fragment analysis—.fsa • HID—.hid Note: The file location specified in a file name convention is used only if a results group is not specified for a well. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 148: Create A New File Name Convention
If factory-provided file name conventions do not suit your needs, you can create new file name conventions: name convention 1. Access the File Name Conventions library. 2. Click Create. Note: You can also create a file name convention from the Assign Plate Contents screen. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 149 • If you are creating the file name convention from the Library, click Save. • If you are creating the file name convention from the Assign Plate Contents screen, click Apply to Plate or Save to Library. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 150: File Name Convention Settings
Name of the file name convention. Names must be unique. Locked When enabled, allows the entry to be unlocked and modified only by the user who created it, the administrator, or another user with unlock permissions. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 151 However, you will see a pre‑check validation error when you start a run if the file name will exceed 240 characters. Delimiters Symbols you can include in the file name: Dash (-), Dot (.), Underscore (_), Plus (+), Dollar ($). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 152: Results Group Library
See “Results Group example 3: store one allelic ladder per run folder (8-capillary instruments)“ on page 160 for a results group example that places three injections in each run folder for 8-capillary instruments. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 153: Create A New Results Group
If factory-provided results groups do not suit your needs, you can create new results groups: Results Group 1. Access the Results Group library. 2. Click Create. Note: You can also create a results group from the Assign Plate Contents screen. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 154 • If you are creating the results group from the Library, click Save. • If you are creating the results group from the Assign Plate Contents screen, click Apply to Plate or Save to Library. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 155: Results Group Settings
Selected Attribute list. Locked When enabled, allows the entry to be unlocked and modified only by the user who created it, the administrator, or another user with unlock permissions. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 156 Sub-folder options: • Include an instrument run name folder (run name can be user-defined in the Load Plates for Run screen) • Include a results group name folder • Include an injection folder 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 157: Results Group Example 1: Store Files By Plate Name
All samples for a plate are stored in the same folder. If you include two plates in a run, a separate folder is created for each plate. Figure 14 PN_Injfolder_RG results group Figure 15 PN_RG results group 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 158: Results Group Example 2: Store Re-Injections In Separate Folders
(see Figure 19). Figure 16 Results group example Figure 17 shows the injection list for a run that specifies duplicate and re-injections. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 159 The numbers in the figure relate the elements in the file name convention with the files created by a run that uses file name convention (see Figure 19). Figure 18 File name convention example 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 160: Results Group Example 3: Store One Allelic Ladder Per Run Folder
Each results group specifies a results group name folder. Because you assign one results group to a set of three capillary instruments) 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 161: Instrument Protocol Library
For information on how changes are tracked if auditing is enabled, see “Audit action“ on page 205. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 162: Create A New Instrument Protocol
Instrument protocol library Create a new If factory-provided instrument protocols do not suit your needs, you can create new instrument protocols: instrument protocol 1. Access the Instrument Protocols library. 2. Click Create. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 163: Instrument Protocol Settings
Dye set Run module Factory-provided modules that specify instrument control parameters. For more information, see Appendix B, “Run modules and dye sets“. Protocol name Name of the protocol. Names must be unique. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 164 Normalization Target proportionately. For example, for an instrument protocol with an injection time of 10 seconds and a Normalization Target of 2000: if you change the injection time to 15 seconds (50% increase), change the Normalization Target to 3000 (50% increase). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 165: Dye Sets Library
For information on how changes are tracked if auditing is enabled, see “Audit action“ on page 205. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 166: Create A New Dye Set
Chapter 7 Manage library resources Dye sets library Create a new dye If factory-provided dye sets do not suit your needs, you can create new dye sets: 1. Access the Dye Sets library. 2. Click Create. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 167: Dye Set Settings
SAE module (described in Chapter 8, “Use Security, Audit, and E-Sig functions (SAE Module)“). Chemistry The standard for which you are creating the dye set: Sequencing Standard or Matrix standard 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 168: Create A New Dye Set Using The Anydye Template
If factory-provided dye sets do not suit your needs, you can create new dye sets: set using the 1. Access the Dye Sets library. AnyDye template 2. Click Create. 3. Enter a dye set name. 4. Select a chemistry and the AnyDye dye set template. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 169 • Example 3—With the Blue, Yellow, and Purple dyes deselected, internal order number is Green (1), Red (2), Orange (3)—the internal order number of Green changes to 1, Red changes to 2, and Orange changes to 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 170: Size Standards Library
For information on how changes are tracked if auditing is enabled, see “Audit action“ on page 205. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 171: Normalization Size Standards Provided
If factory-provided size standards do not suit your needs, you can create new size standards: standard 1. Access the Size Standards library. 2. Click Create. 3. In the Create New Size Standard dialog box (Figure 22), enter a size standard name. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 172: Modify A Factory-Provided Normalization Size Standard
2. Click Duplicate. standard 3. Edit the copy of the normalized size standard. The size standard peaks used to normalize the data are displayed in gray and are not editable. 4. Click Save. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 173: Basecalling Protocols Library (Primary Analysis-Sequencing)
1. Access the Basecalling Protocols library. 2. Click Create. 3. In the Analysis Settings tab of the Create New Basecalling Protocol dialog box (Figure 23), specify settings “Basecalling protocol—Analysis settings“ on page 176. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 174 – If any values are in the fail range, the QV flag in Monitor Run is set to (red). • View Sequencing Results4Metric Analysis Results table—The pass/check/fail status for Trace Score Quality, CRL Quality, and QV20+ Quality results. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 175 Chapter 7 Manage library resources Basecalling protocols library (primary analysis—sequencing) 5. Click Save. Figure 23 Create New Basecalling Protocol—Analysis Settings 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 176: Basecalling Protocol-Analysis Settings
The version listed in sequencing results is a 4-digit number. The fourth digit is an internal number used by the software. Mobility file Compensates for mobility differences between dyes used to label the DNA. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 177 • Flat Profile—The processed traces are scaled semi-locally so that the average height of peaks in any region is about equal to a fixed value. The profile of the processed traces will be flat on an intermediate scale (> about 40 bases). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 178: Basecalling Protocol-Qv Settings
For information on how changes are tracked if auditing is enabled, see “Audit action“ on page 205. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 179: Create A New Sizecalling Protocol
(Figure 25), specify settings (see “Sizecalling protocol—Analysis settings“ on page 181). 4. Click QC Settings. In the QC Settings tab of the Create New Sizecalling Protocol dialog box (Figure 26), specify settings (“Sizecalling protocol—QC settings“ on page 184). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 180 Size Quality flags. Specify analysis settings that accurately detect and size the size standard, and QC settings with appropriate pass fail ranges. The 3500 Series Data Collection Software 3.1 does not support re-analyzing data with new settings. Figure 25 Create New Sizecalling Protocol—Analysis Settings...
Page 181: Sizecalling Protocol-Analysis Settings
Size standard definition in the software that corresponds to the dye set used in the chemistry. To apply normalization, select a normalization size standard (see “Normalization size standards provided“ on page 171). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 182 175 are detected. Peaks with heights below 175 are still displayed in the electropherogram plots but are not detected or labeled. Note: Use the same peak amplitude thresholds in secondary analysis software. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 183 • The Peak Window Size setting is limited to odd numbers. To increase peak detection sensitivity: Increase polynomial degree, decrease peak window size. To decrease peak detection sensitivity: Decrease polynomial degree, increase peak window size. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 184: Sizecalling Protocol-Qc Settings
• Within ±Y data point (pull-up scan) of the major peak When at least one peak is identified as a pull-up peak, the (Check) flag is displayed for the Spectral Pull-Up quality flag in View Fragment Results. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 185: Qc Protocols Library (Primary Analysis-Hid)
(Figure 27), specify settings (“QC protocol—Analysis settings“ on page 187). 4. Click QC Settings. In the QC Settings tab of the Create New QC Protocol dialog box (Figure 28), specify settings (“QC protocol—QC settings“ on page 190). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 186 IMPORTANT! Normalization is not applied to samples with Size Quality flags. The 3500 Series Data Collection Software 3.1 does not support re-analyzing data with new settings. Figure 27 Create New QC Protocol—Analysis Settings...
Page 187: Qc Protocol-Analysis Settings
Sizing Range specified below. Sizing Range Select Partial, then specify 80 to 400 to limit the fragment sizes evaluated for the size standard. If you specify sizes outside this range, the Sizing Quality may fail. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 188 175 are detected. Peaks with heights below 175 are still displayed in the electropherogram plots but are not detected or labeled. Note: Use the same peak amplitude thresholds in secondary analysis software. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 189 0° (horizontal line). A value other than 0 moves the peak end point toward its center. The value entered in this field must be non-positive. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 190: Qc Protocol-Qc Settings
Enter the maximum peak width (in base pairs). When a peak width is greater than the threshold, the (Check) flag is displayed for the BD (Broad Peak) quality flag in View HID Results. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 191: Chapter 8 Use Security, Audit, And E-Sig Functions
You can configure the SAE module in a variety of ways: • Require multiple e-sigs. • Require specific users or users with specific permissions to e-sign. • Allow only certain users to approve reviewed samples. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 192: Configure The Security System
The Security screen allows you to control restrictions and security policies for all user accounts, and set up notifications when certain security events occur. Access the Security screen. Figure 29 Security screen 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 193 For information, see “Set up messaging notifications“ on page 194. 7. Click Save Settings. The new settings are applied to the logged-in user the next time the user logs in. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 194 • Session timeout for a user—No activity occurred in a user account for the specified period of inactivity. • Account suspension for failed authentication—The user exceeds maximum number of allowed failed authentications (login attempts with an incorrect password). • Notification for SAE activation —Not supported. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 195: Manage User Accounts
The software includes a default Administrator user account with permissions (defined by the account user role) to perform all functions in the software. Create a user account 1. Access the Users screen. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 196 • Dx User (not supported in research • Password Change Date (by either use only mode.) user or administrator) • Role • Email (for records only) • Status • Phone • Password Expired (true=yes, • Comments false=no) 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 197 Three default user roles are included in the software. You can modify two of them, and can create your own roles with customized settings as needed: • Administrator (cannot be edited or deleted) • Scientist • Technician 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 198 Create plate/plate template • Start plate run • Edit default instrument run name • Manage injection list • Duplicate injection • Re-inject • Edit sample (names) Primary Analysis • Export sequencing results 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 199 Log in to timed-out user sessions Edit a user role 1. In the Roles screen, select a user role, then click Edit. 2. Edit settings as needed. You cannot edit the Administrator user role. 3. Click Save. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 200 3. To print the report, click Print. Close the report. Save electronic copies (pdf) of the report To save the report electronically (.pdf), print the report and select CutePDF Writer as the printer. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 201: Manage Auditing
The Audit Settings screen controls the events that are audited, and the reasons available to users when audit mode is set to Prompt or Required. Access the Audit Settings screen. Figure 30 Audit Settings 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 202 • Required—The event is audited, a reason prompt is displayed, and the user must specify a reason. • Silent—The event is audited, no reason prompt is displayed. 3. Click Save Settings. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 203 (displayed when a user performs an audited action), select the Select a reason from the list for your change checkbox. Users are not permitted to enter a reason. 2. As needed, click Create, or select a reason, then click Edit or Delete. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 204: Generate Audit Reports
• Select a record, then click Show Object History or Show Audit Details. • In the history dialog box, select a record, then click Show Audit Details. • Click Table Settings, then specify the columns to show or hide. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 205 Object Audit Detail History. • Items within other items—The deletion of an item from within another item is audited. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 206 “check after” or “prompt before” function • Enable e-signature E-Signature settings Update • Disable e-signature • Modify e-signature settings E-Signature type Update • Modify the enable state of an E- Signature Type 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 207 Maintenance Wizards • Change Polymer Type Wizard started • Change Array Wizard started • Replenish Polymer Wizard started • Fill Polymer Wizard started • Water Wash Wizard started • Instrument Shutdown Wizard started 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 208 View and print audit reports 1. Display the records of interest. 2. Filter the list to decrease the time required to generate reports. IMPORTANT! You cannot cancel a report after you click a view button. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 209 IMPORTANT! If you change font settings before you generate a report, the report may not be generated. Generate the report again. 6. To save the report electronically (.pdf), print the report and select CutePDF Writer as the printer. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 210 Note: If you export audit records for samples that are not in their original location (samples have been deleted or moved), an error message is displayed. Return sample data files to their original location, then export again. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 211: Manage Electronic Signature (E-Sig)
Manage electronic IMPORTANT! Changes to e-signature settings are not activated until you log out of signature (E-sig) the software, then log back in. Access the E‑Signature Settings screen Access the E-Signature Settings screen. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 212 By default, each required signature needs no special authority; any user can sign. • Click Apply. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 213 Function to check E-Signature type required (defaults if before enabled) Approve Spatial Calibration Start Run 1 signature, any authorities (any user, any user role) Approve Spectral Calibration Approve Plate Approve Sequencing Install Standard Results 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 214 • Any other user with the Scientist role specified and electronic signature enabled in their user account If a user that does not meet the specified criteria signs, a message is displayed to indicate which users have e-signed. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 215 • Approve Microseq ID Install • Approve Basecall Protocol Standard Results • Approve QC Protocol • Approve Fragment Install Standard • Approve Assay Results • Approve Plate Template • Approve HID Install Standard Results 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 216 Export e-sig records As needed, you can export e-sig records to a .txt file for additional manipulation and reporting outside the 3500 Series Data Collection Software 3.1. 1. Display the records of interest as described in “Display e-sig records“ on page 215.
Page 217: Export And Import User Accounts Security Audit And Electronic Signature Settings
– User Roles—All user roles and associated permissions 3. Click Export. 4. Specify the name and location for the exported .dat file, then click Save. A message is displayed when the export completes. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 218: Users
• Electronic signature (e-sig)—Requires users to provide a user name and password when performing certain functions. Depending on the way that your administrator configures these features, you may see the following dialog boxes and prompts when you use the software. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 219: Security
When your password is about to expire, a message is displayed when you log in. To change your password, select Tools4Change Password. Enter your current password, enter the new password two times, then click OK. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 220 Log In dialog box indicates that your user session has timed out. You must enter your user name and password to access the software. Note: The administrator or another user with permission to log in to timed-out sessions can click Reset, then log in. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 221: Audit
• The E-Signature button is enabled in the library or the calibration. • You are prompted to sign as described in “How the software prompts electronic signature before a run“ on page 214. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 222 Chapter 8 Use Security, Audit, and E-Sig functions (SAE Module) Users • The Open Plates dialog box or the library displays an “Is signed” column that reflects the e-sig status of an item. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 223: Chapter 9 Maintain The Instrument
IMPORTANT! Use only the cleaning agents listed in this guide. Use of cleaning agents other than those listed in this guide may damage the instrument. 1. Review the calendar reminders list in the Dashboard daily, then perform the Review calendar scheduled tasks. reminders 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 224: Daily Instrument Maintenance Tasks
Check the loading-end header to ensure that the capillary “Install or change the capillary tips are not crushed or damaged. array“ on page 235 Ensure that the pump block is in pushed back position. Daily Figure 31 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 225: Weekly Instrument Maintenance Tasks
If Security, Audit, and E-sig is enabled, archive and purge “Archive and purge“ on page 210 audit records. Defragment the hard drive. Monthly, or before “Defragment the computer hard fragmentation drive“ on page 246 reaches 10% 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 226: Quarterly Maintenance Tasks
• Flush pump trap You can change the priority of factory tasks, but you cannot remove them from the calendar or alter the frequency at which the notifications for the tasks are displayed. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 227: Create Calendar Entries
2. Click Planned Maintenance Report. Report 3. Specify the date range, then click OK. 4. Select Print as needed. 5. To save the report electronically (.pdf), print the report and select CutePDF Writer as the printer. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 228: Review The Notifications Log
Dashboard (see “Review calendar reminders“ on page 223). 1. Access the Notifications Log. 2. View the Notification Log Report and print as needed. Note: Multi-column sorting is supported (see “Sort by one or multiple columns“ on page 76). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 229: Clean The Instrument
Do not remove the seal until you have completed step 5. 3. Verify that the seal is intact. Do not use if buffer level is too low or seal has been compromised. A fill tolerance of ±1 mm is acceptable. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 230: Install The Cathode Buffer Container (Cbc)
4. Check that the seal is intact. Do not use if the buffer level is too low or the seal has been compromised. A fill tolerance of ±0.5 mm is acceptable. Fill line 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 231 IMPORTANT! Ensure that the washing septum is securely seated to prevent displacement of the septum during operation. 10. Click the Tray button on the front panel to move the autosampler to the front position. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 232: Replenish, Change, Flush, And Store Polymer
2. Allow the refrigerated polymer to equilibrate to room temperature (15–30°C) before use. 3. In the Dashboard, click Wizards, then click Replenish Polymer (requires 10 to 20 minutes) or Change Polymer Type (requires 60 to 70 minutes). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 233 5. When instructed to install the polymer, peel off the seal at the top of the pouch fitment. Note: You may notice a tiny droplet of polymer inside the fitment (residual from the pouch filling process). This is not expected to cause any performance issues. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 234: Store Partially Used Polymer
3. Follow the prompts in the Fill Array wizard window. 4. Click Refresh in the Dashboard to update the screen. 5. Check the Quick View section of the Dashboard for updated status after filling of the capillary array with fresh polymer. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 235: Change And Store A Capillary Array
2. In the Maintenance wizards screen, click Install Capillary Array. 3. Follow the prompts in the Install Capillary Array wizard window. 4. Check the Quick View section of the Dashboard for updated status of the capillary array. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 236: Store A Capillary Array
• The pump assembly is exposed to temperatures greater than 40°C, which can damage the pump components. • There is arcing in the pump assembly, which can damage the acrylic pump material. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 237: Remove Bubbles From The Polymer Pump
– the lower polymer block may need to be replaced by Thermo Fisher Scientific. • A contaminant in the polymer delivery pump is suspected of causing problems. The check valve fitting might be clogged or contaminated. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 238: Flush The Water Trap (Pump Trap)
Pump Cleaning Kit , Cat. No. 4414007 ) with distilled or deionized water. Expel any bubbles from the syringe. IMPORTANT! Do not use a syringe smaller than 20 mL. Doing so may generate excessive pressure within the trap. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 239 6. Remove the syringe from the Luer fitting. Hold the fitting with one hand while turning the syringe counterclockwise with the other hand. 7. Close the Luer fitting by lightly turning clockwise until the fitting seals against the block. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 240: Shutdown Move And Reactivate The Instrument
> 2 weeks 1. Run the Install Capillary wizard and store the capillary array. 2. Clean any spills or residual polymer. 3. Run the Shutdown the Instrument wizard. 4. Unplug the instrument. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 241: Move And Level The Instrument
6. Have an IQ OQ performed before using the instrument. IMPORTANT! After performing a conditioning wash, ensure that the buffer level inside the ABC is at or above fill line before proceeding to the next step. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 242: Reactivate The Instrument
Select a location other than the install directory for the datastore backup. IMPORTANT! Do not back up the datastore to the installation directory. The installation directory is deleted during the uninstall. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 243: Archive, Purge, And Restore Data
1. Access the Archive screen. 2. Specify the date category, specify a date range that is earlier than the date on which you made the duplicates of the library items you want to retain, then click 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 244 3. Specify a location and file name for the archive (.dsz) file, then click Save. IMPORTANT! Do not specify <<install directory>>:\Applied Biosystems\3500\datastore as the archive location. If you do so, your archive can be deleted if you uninstall the software.
Page 245: Monitor Disk Space
Automatic disk space check before a run Before a run, the software checks free disk space and displays a message when the hard disk is 70–75% full. At 78% full, the software will not start a run. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 246: Manage Software Licenses
Note: You can click Analyze to see if you should defragment or not. Manage software licenses The 3500 Series Data Collection Software 3.1 requires a license to run. IMPORTANT! If you replace or add a network card in the computer running the software or relocate the software to a new computer, contact Thermo Fisher Scientific to update your license for the new network card or computer.
Page 247 Collection Software 3.1 (see “Step two: Start the 3500 Series Data Collection Software 3.1“ on page 31). 3. Obtain the license key. The license key is provided on the 3500 Series Data Collection Software 3.1 CD case, or in an email from Thermo Fisher Scientific.
Page 248: Renew A Software License
5. Obtain the renewed software license file from your email. 6. Copy the renewed software license file to the desktop of this computer. 7. If the Software renewal dialog box has closed, access it by selecting Manage4License Manager. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 249: Service Log And Usage Statistics
10. Click Close. Service Log and Usage Statistics The Service Log and Usage Statistics functions are for use by Thermo Fisher Scientific service engineers at the time of service. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 250 Thermo Fisher Scientific service representative. IMPORTANT! See “Safety and electromagnetic compatibility (EMC) standards“ on page 306 for instrumentation and chemical safety information and guidelines. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 251: Appendix A Troubleshoot
• If software operations are taking longer than expected When you are instructed to restart the instrument and the computer: 1. Exit the 3500 Series Data Collection Software 3.1. 2. Power off the computer. 3. Make sure the instrument door is closed, then power off the instrument.
Page 252: Instrument Components
Figure 31 Instrument interior Detection cell heater block Polymer delivery pump (PDP) Anode buffer container (ABC) Polymer or conditioning pouch Cathode buffer container (CBC) Oven door Capillary array Oven condensation reservoir Autosampler 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 253 Figure 32 Polymer delivery pump (PDP) Upper polymer block Buffer-pin valve Lower polymer block Anode buffer container (ABC) Array locking lever Water trap waste container Check valve fitting Polymer pouch lever Polymer pouch Drip tray 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 254: Instrument Troubleshooting
See “Prepare the plate assembly“ on page 53. IMPORTANT! If array tips are bent, replace the array. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 255 Thermo Fisher Scientific. If the lever moves up and down freely, push the upper polymer block all the way back against the wall. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 256 238 and “Wash the pump chamber and channels“ on page 237. If the problem persists, contact Thermo Fisher Scientific. Figure 35 Pump chamber and valve fitting Debris in chamber Check valve fitting 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 257 Wipe away spills, moisture, and Condensation on the CBC. the oven condensation with a lint-free lab Condensation around the septa. cloth. If the problem persists, contact • An error message regarding Thermo Fisher Scientific. electrical current 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 258: Rfid Troubleshooting
Ensure that label is close, and parallel, to the instrument. Reposition or re-install pouch, then click Refresh on the Dashboard. Restart the instrument and the computer (see “Restart the instrument and the computer“ on page 251). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 259: Error Messages
Reagent Pouch after removing a used or a partially used polymer pouch. Completely remove the top seal of the Polymer pouch or Conditioning Reagent Pouch before use. If the problem persists, contact Thermo Fisher Scientific. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 260 Close the Java update scheduler. message complete the update. Note: The Java update scheduler does not affect the performance of the 3500 Series Data Collection Software 3.1 or the quality and accuracy of the data collected. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 261: Dashboard Troubleshooting
RFID issue. Restart the instrument and the expired, but expiry date on computer (see “Restart the consumable indicates it is not instrument and the computer“ on expired. page 251). Contact Thermo Fisher Scientific 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 262: Software Troubleshooting - General
You must select a plate template from Go to Define Plate Properties As) when you edit a plate template the main workflow to edit it. screen4Open Plate4Edit Existing from the library. Template. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 263 Notification log in Calendar Settings are not migrated. Manually update settings after Reminders is not retained after data migration. migration from v1.0 to v3 software. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 264: Run, Re-Run, Or Re-Inject Troubleshooting
Replace the capillary array. Failed reaction Repeat reaction. Low signal. Degraded formamide. Use a fresh aliquot of Hi‑Di ™ Formamide (see “Hi‑Di ™ Formamide“ on page 22 for storage conditions). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 265 Tighten the connectors and array locking lever. No current. Not enough buffer in ABC. Ensure that the buffer is filled up to the fill line. See “Check buffer fill levels“ on page 34. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 266 Possible contaminant in sample. Re-amplify the DNA. Sample re-naturation. Heat-denature the sample in properly stored formamide (see “Hi‑Di ™ Formamide“ on page 22 for storage conditions) and immediately place on ice. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 267: Review Results Troubleshooting
At least one file is not in the correct Select individual folders or files for select multiple folders for import format for import, therefore no files import instead of multiple folders. are imported. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 268 Sample Peak Dye and Sample Peak columns. the column headers are shifted to the values is incorrectly named, and the right. column headers after Dye/Sample are shifted one column to the right. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 269: Link/Load Plate Troubleshooting
In the example below, the installation and recommended replacement dates for cathode buffer are identical to the dates for anode buffer. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 270: Assign Plate Contents Troubleshooting
Error message is displayed when you Plate is not saved. Save the plate, close the plate, open export a newly created plate from the the plate, then export. Assign Plate Contents screen. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 271: Spatial Calibration Troubleshooting
Do not preheat the oven before running the spatial calibration. Accept/Reject buttons are dimmed. Communication problem between the Restart the instrument and the computer and instrument. computer (see “Restart the instrument and the computer“ on page 251). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 272: Spectral Calibration Troubleshooting
Septa contamination. Replace the CBC septa. view appear to be in the wrong order or there are extraneous peaks IMPORTANT! Make sure to replace the CBC septa as part of monthly maintenance. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 273 (for each dye set) after installing a new capillary array, you may notice pull-down peaks (or mirror image peaks). These pull- down peaks will eventually correct themselves once the run completes. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 274: Sequencing Install Standard Troubleshooting
Check the expiration date and storage button is active. reagents. conditions of the sequencing standard and/or reagents. If necessary, replace with a fresh lot. Bubbles in the polymer system. Run the Remove Bubbles wizard. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 275: Fragment/Hid Install Standard Troubleshooting
Check the expiration date and storage reagents. conditions of the matrix standards and/or reagents. If necessary, replace with a fresh lot. Bubbles in the polymer system. Select the Bubble Remove wizard to clear the bubbles. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 276: Monitor Run Troubleshooting
Re-inject. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 277: Audit Troubleshooting
Comments field. dye set calibrated. Electronic signature prompt is Electronic signature prompt is No action. displayed when you edit sample displayed for sample comments, comments. regardless of the electronic signature setting. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 278: Manual Commands Troubleshooting
3. Navigate to s:\TroubleshootData, then email the data-<yyyy-mm-dd-hh-mm-ss- mmm>.tslog file to your Thermo Fisher Scientific representative. View the log files Use a text editor (such as Wordpad) to view the 3500 Series Data Collection Software 3.1-generated log files: Log file...
Page 279: View Instrument Sensor Details
Click View Instrument Sensor Details in the Dashboard to display instrument information. sensor details Figure 36 Instrument sensor details Run status of the instrument is displayed while a run is in progress. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 280: Review Error Message Details
Appendix A Troubleshoot Troubleshooting procedures Review error Error messages in the 3500 Series Data Collection Software 3.1 include a Details button. message details Click Details to display more information about an error message. Reset the Resetting powers off, then powers on, the instrument. Reset the instrument when: instrument •...
Page 281: Run Modules
POP-6 ™ £65 ³168 ³504 ³450 sequencing BDxRapidSeq50_POP6xl BigDye XTerminator ™ BDxRapidSeq50_POP7 POP-7 ™ £40 ³280 ³840 ³500 BDxRapidSeq50_POP7xl Rapid BDxRapidSeq36_POP4 POP-4 ™ £45 ³240 ³720 ³400 sequencing BDxRapidSeq36_POP4xl BigDye ™ XTerminator 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 282 POP-7 ™ £125 ³88 ³264 ³850 sequencing MicroSeq50_POP7xl Throughput (Samples / Day): The total number of samples run in 23 hours (0.5 hour for user interaction and 0.5 hour for warm-up time). 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 283 POP-6 ™ <0.15 <0.30 £60 ³184 ³552 £60 analysis POP6 to ³400 FragAnalysis36_ POP6xl Long frag. LongFragAnalysi POP-7 ™ <0.15 <0.30 <0.45 £125 ³88 ³264 £40 analysis s50_POP7 to ³700 LongFragAnalysi s50_POP7xl 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 284: Dye Sets
Table 8 Fragment analysis dye sets dye sets for all Application applications ™ SNaPshot DNA sizing for 5-dye chemistry DNA sizing for 6-dye chemistry DNA sizing for 4-dye chemistry DNA sizing for 4-dye chemistry AnyDye DNA sizing 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 285: Hid Analysis Dye Sets
™ Express • SEfiler Plus ™ • Sinofiler ™ • Yfiler ™ • Yfiler ™ Direct • Other 5-dye kits 6-dye: • GlobalFiler ™ ™ • GlobalFiler Express • NGM Detect ™ 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 286: Appendix C Instrument Specifications
• Laser Output power 20mW • Beam divergence 1.4 mrad • Emitting color Natural White • Luminous Intensity 250 Cd Electrophoresis Voltage Up to 20 kV Oven Temperature Active temperature control from 18°C to 70°C 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 287: Environmental Requirements
15–30°C (59–86°F) (Room temperature should not fluctuate ±2°C during an instrument run) 20–80% relative humidity, noncondensing Transport and storage –30 to +60°C ( –22 to +140°F) Minimum 20% relative conditions humidity, maximum 85% (non-condensing) 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 288: Power And Communication Connections
Appendix C Instrument specifications Power and communication connections Power and communication connections Ethernet port for computer instrument connection Circuit breaker Connector for instrument power cable 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 289: Appendix D Catalog Numbers
Retainer and base (Standard), 96-well RUO 4410228 Retainer and base (Fast), 96-well RUO 4409530 Retainer and base (Standard), 384-well, RUO 4410235 Septa, 8-strip RUO 4410701 Septa, 96-well 4410700 Septa, 384-well RUO 4412520 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 290: Instrument Consumables
Terminator v1.1 Matrix Standard Kit 4336824 BigDye ™ Terminator v1.1 Cycle Sequencing Kit 4337449 ™ BigDye Terminator v3.1 3500/3500xL Sequencing Standards, BigDye ™ Terminator v3.1 4404312 BigDye ™ Terminator v3.1 Matrix Standard Kit 4336974 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 291: Fragment And Hid Analysis Reagents
401734 GeneScan ™ 600 LIZ ™ Size Standard v2.0 4408399 ™ ™ GeneScan 1200 LIZ Size Standard 4379950 AmpFℓSTR ™ Identifiler ™ Allelic Ladder (For HID install check) Contact Thermo Fisher Scientific 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 292: Appendix E Limitations
Limitations The 3500 instrument contains the limitations noted below. Please ensure that any use of the instrument takes into consideration these limitations. General • IMPORTANT! Enter only alpha-numeric characters in the software. Special characters may not be correctly displayed in some software screens, may cause problems with plate, file, folder, user account, and/or library item names, and may interfere with starting a run and/or importing and exporting library items.
Page 293: Instrument And Consumables
• Changes to e-signature settings are not activated until you log out of the software, then log back in. • If you change font settings before you generate an Object Audit report, the report may not be generated. Generate the report again. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 294: Review Results
Dye/Sample are shifted one column to the right. You can edit the exported file: Cut/paste column headers one column to the right, enter correct headers for the Dye and Sample Peak columns. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 295: Appendix F Radio Frequency Identification (Rfid) Technology
WARNING! Radio frequency identification (RFID) signals from external devices could possibly disrupt the operation of the 3500 RFID read/write units. RFID signals from the 3500 RFID read/write units could possibly disrupt the operation of external RFID devices.
Page 296: Locations Of Rfid Read/Write Units
3. Re-read the written data on the tags to confirm that it is accurate, using a checksum to verify data integrity. The RFID read/write units perform the functions listed above at the start of each 3500 Series Data Collection Software 3.1 run.
Page 297: Specifications
3 feet instrument from other wireless technologies • RFID tag read/write/re-read with checksum Wireless security • Password access for use of software • Base-64 encoding of data between the instrument and the computer 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 298: Troubleshooting
• If the instrument can read the RFID label, install a new CBC, ABC, pouch, or array. • If the instrument cannot read the RFID label, contact Thermo Fisher Scientific. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 299: Appendix G Normalization
Normalization Overview of the normalization feature For fragment analysis applications, the 3500 Series Data Collection Software 3.1 includes an optional normalization feature for use with the GeneScan ™ 600 LIZ ™ Size Standard v2.0 (GS600 LIZ v2). This feature attenuates signal variations associated with instrument, capillary array, sample salt load, and injection variability between capillaries and instruments.
Page 300: When To Use The Normalization Feature
When to use the normalization feature When to use the normalization feature The 3500 Series Data Collection Software 3.1 provides three normalization size- standard definition files that you can specify for primary analysis of samples prepared with the GS600 LIZ v2 size standard and the G5 and J6 dye sets: •...
Page 301: Appendix H Safety
Consult the manual for further safety Consulter le manuel pour d’autres information. renseignements de sécurité. Caution, risk of electrical shock Attention, risque de choc électrique Caution, piercing hazard Attention, danger de perforation 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 302: Conformity Symbols
à la clientèle pour des renseignements sur les options d’élimination responsable. Conformity Conformity mark Description symbols Indicates conformity with safety requirements for Canada and U.S.A. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 303: Safety Alerts On This Instrument
3B (III) présent en invisible laser radiation position ouverte et avec les present when open and dispositifs de sécurité non interlocks defeated. enclenchés. Éviter toute Avoid exposure to exposition au faisceau. beam. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 304: Instrument Safety
Physical injury CAUTION! Moving Parts. Moving parts can crush, pinch and cut. Keep hands clear of moving parts while operating the instrument. Disconnect power before servicing. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 305: Electrical Safety
· Before using any cleaning or decontamination methods (except those recommended by the manufacturer), users should confirm with the manufacturer that the proposed method will not damage the equipment. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 306: Laser
WARNING! LASER HAZARD. Under normal operating conditions, the ™ Applied Biosystems 3500/3500xL Genetic Analyzer is categorized as a Class 1 laser product. However, removing the protective covers and (when applicable) defeating the interlock(s) may result in exposure to the internal Class 3 B laser.
Page 307: Emc
Directive 2011/65/EU European Union “RoHS Directive” – Restriction of hazardous substances in electrical and electronic equipment Radio compliance Reference Description Directive 2014/53/EU European Union "RE Directive" - Radio equipment (as of June 12, 2017) 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 308: Chemical Safety
Ensure that the waste is stored, transferred, transported, and disposed of according to all local, state/provincial, and/or national regulations. · IMPORTANT! Radioactive or biohazardous materials may require special handling, and disposal limitations may apply. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 309: Biological Hazard Safety
U.S. Department of Health and Human Services, Biosafety in Microbiological and Biomedical Laboratories (BMBL), 5th Edition, HHS Publication No. (CDC) 21-1112, Revised December 2009; found at: www.cdc.gov/biosafety/publications/bmbl5/BMBL.pdf · World Health Organization, Laboratory Biosafety Manual, 3rd Edition, WHO/CDS/CSR/LYO/2004.11; found at: www.who.int/csr/resources/publications/biosafety/Biosafety7.pdf 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 310: Documentation And Support
Obtaining support For service and technical support: • Call Toll-Free in US: 1 800 955 6288 • Email instrumentservices@lifetech.com For the latest services and support information for all locations, go to: thermofisher.com/support 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 311: Limited Product Warranty
Life Technologies Corporation and/or its affiliate(s) warrant this product as set forth ™ in the Applied Biosystems 3500/3500xL Genetic Analyzer – Instrument Limited Warranty. If you have any questions, please contact Life Technologies at thermofisher.com/ support. 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 312: Additional Instrument Symbols
UPPER LIMIT OF OF TEMPERATURE TEMPERATURE DO NOT REUSE BIOLOGICAL RISKS CAUTION, CONSULT CONSULT INSTRUCTIONS ACCOMPANYING FOR USE DOCUMENTS UPPER AND LOWER LIMITS OBSERVE PRECAUTIONS FOR OF HUMIDITY HANDLING ELECTROSTATIC SENSITIVE DEVICES 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 313: Index
45 user 195 plate view 47, 73 action log, contents 207 results group 77 Administrator user role 197 sample type 47 Advanced setup table view 75 preference 37 template for 79 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 314 Basepair Accuracy 127 do not rename 17 Basic setup, preference 37 maintain 242 BigDye Terminator kits and standards 290 name requirement 17, 27, 29 biohazard safety 309 restart 251 borrowing start up 29 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 315 221 data troubleshooting 264 overview 218 datastore, backup during install or uninstall 242 signing 221 date format, setting 37 electropherogram troubleshooting 264 default settings, specifying 37 environmental requirements 287 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 316 Flat Profile 176 plate 44, 79 fragment analysis dye sets 284 sample files, fragment 84, 94 security settings 218 reagents, part numbers, storage conditions 291 user account settings 218 results, review 91 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 317 65 template 139 pause after last injection 37 template, create new item from 140 view audit records 141 preview 64 start 64 view e-sig records 141 start with existing plate 58 license 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 318 244 non-linearity in large fragment size standards 184 defragment 246 normalization disk space, monitor 245 and SQ (sizing quality) 184, 190 library items, archive, purge, and restore 243 factor 96 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 319 80 permissions, user account 197, 219 specify 42, 144 planned maintenance schedule 226 plate view planned maintenance tasks 227 assign plate contents 47 plate customize 74 384-well assembly 56 plate-to-capillary map 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 320 QV (average quality value), monitor run 67 sample quality reports 101 spatial calibration report 107, 119 See also average quality value [QV (average qual- spectral calibration 107, 120, 130, 137 ity value) 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 321 267 e-sig 216 zoom 97, 115 export sequencing 90 review results, fragment/HID fragment results 101 modify data in secondary analysis software 90, install check 130, 137 plate grid 50 normalized data 96 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 322 47 See also review results, sequencing sample name sequencing analysis assign 75 reagents, part numbers and storage conditions fill and fill series 75 sample plate. See plate dye sets 284 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 323 206 activate 246, 248 system defaults, date format 27 obtain 246, 248 system specifications 286 See also license, software system start up 28 sort tables, multi-column 76, 100, 141 spatial calibration 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 324 271 spectral calibration 272 workflow, basic setup, preference 37 view instrument sensor details 279 troubleshooting, audit 277 TroubleshootingUtility.bat 278 zoom True Profile 176 fragment plots 97 plate view 74 spectral calibration 114 3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1...
Page 326 thermofisher.com/support | thermofisher.com/askaquestion thermofisher.com 25 October 2018...

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3500xl

Applied Biosystems 3500 User Manual

CHAPTER 1 Instrument and Software Description

CHAPTER 2 Start the System

CHAPTER 3 Set up and Run

CHAPTER 4 Review Sequencing Results

CHAPTER 5 Review Fragment/Hid Analysis Results

CHAPTER 6 Run Calibrations and Install Checks

CHAPTER 7 Manage Library Resources

CHAPTER 8 Use Security, Audit, and E-Sig Functions

CHAPTER 9 Maintain the Instrument

Quick Links

Troubleshooting

Need help?

Questions and answers

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Summary of Contents for Applied Biosystems 3500