QUICK REFERENCE OpenArray Sample Tracker Software For QuantStudio 12K Flex OpenArray Sample Block and the OpenArray Real-Time PCR System Publication Part Number 4460657 Rev. C Revision Date May 2012 Contents Product information.................................................................................................. 1 Supported instruments and plates..................................................................................... 3 Workflow............................................................................................................ 4 Start the software.................................................................................................... 5 (Optional) Set preferences............................................................................................. 6 Enter experiment properties.......................................................................................... 7 Enter sample information for the 96-well reaction plates................................................................. 9 View the sample mapping............................................................................................ 11 Print or export data................................................................................................. 15 Close the software.................................................................................................. 20 Create *.csv files.................................................................................................... 21 Product information Overview To load samples into a TaqMan OpenArray plate, you must: 1. Pipet the samples into a 96-well reaction plate. 2. Transfer the samples from the 96-well reaction plate to an OpenArray 384-Well Sample Plate using an adjustable or fixed pipette. 3. Transfer the samples from the OpenArray 384-Well Sample Plate to the TaqMan OpenArray plate using the OpenArray AccuFill System. IMPORTANT! To ensure accurate results, you need to correctly track sample information from plate to plate. The OpenArray Sample Tracker Software helps you easily track your samples. Enter sample information for the 96-well reaction plate into the Sample Tracker Software. The Sample Tracker Software automatically maps the sample information to the appropriate locations in the OpenArray 384-Well Sample Plate, providing a pipetting guide and the TaqMan OpenArray plates, for your records. Software terms The following terms are used in the Sample Tracker Software: 384-well sample plate The OpenArray 384-Well Sample Plate used in the OpenArray AccuFill System. Sample mapping The process of moving sample information from the 96-well reaction plate(s) to the OpenArray 384-Well Sample Plate and subsequently to the TaqMan OpenArray plates. Sample integration A function in the OpenArray AccuFill Software which adds sample information from a 384-well plate file (*.csv) to the assay information in an OpenArray plate file (*.spf or *.tpf) to create an integrated OpenArray plate file (*.spf or *.tpf). Fixed 12-channel pipette A 12-channel pipette where the distance between the tips is set for a 96-well plate. A pipette of this type skips every other well in a 384-well plate. Adjustable 12-channel pipette A 12-channel pipette where the distance between the tips is adjustable. A pipette of this type can be set to pipet into adjacent wells for either a 96- or 384-well plate.
Screen captures Unless otherwise indicated, the screen captures in this document illustrate the workflow for a TaqMan OpenArray Genotyping Plate Format 64. 2
Supported instruments and plates Supported instruments Applied Biosystems OpenArray Real-Time PCR System Applied Biosystems QuantStudio 12K Flex Real-Time PCR System Supported OpenArray plates OpenArray plate Plate names Format No. of preloaded assays Maximum no. of samples OpenArray plate Part no. OpenArray system QuantStudio 12K Flex system TaqMan OpenArray Genotyping Plates TaqMan OpenArray Real- Time PCR Plates TaqMan OpenArray 3 Sample Fixed Panels Plates TaqMan OpenArray 4 Sample Fixed Panels Plate N/A N/A Format 18 18 (in triplicate) TaqMan OpenArray Human MicroRNA Panel Plate TaqMan OpenArray Rodent MicroRNA Panel Plate TaqMan OpenArray Human Kinome Panel TaqMan OpenArray Human Cancer Panel TaqMan OpenArray Human Inflammation Panel TaqMan OpenArray Human Stem Cell Panel TaqMan OpenArray Human Signal Transduction Panel TaqMan OpenArray Mouse Inflammation Panel Format 16 16 144 4413546 4471113 Format 32 32 96 4413548 4471114 Format 64 64 48 4413550 4471115 Format 128 128 24 4413551 4471116 Format 192 192 16 4413553 4471117 Format 256 256 12 4413554 4471118 48 4456272 4471124 Format 56 56 48 4456276 4471125 Format 112 112 24 4456268 4471126 Format 168 168 16 4456270 4471127 Format 224 224 12 4456274 4471128 Format 818 N/A 3 4470187 Format 818 3 4470188 Format 896 3 4467775 Format 672 4 4467778 Format 672 4 4467776 Format 672 4 4467777 Format 672 4 4467779 Format 672 4 4467780 N/A = Not applicable 3
Workflow Start the software (page 5) Enter experiment properties (page 7) Enter sample information for the 96-well reaction plates (page 9) View the sample mapping (page 11) Print or export data (page 15) 4
Start the software Standalone version 1 2 Download the software a. Go to www.lifetechnologies.com and click the Technical Resources tab. b. Click Software, Patches, and Updates. c. Click OpenArray Sample Tracker Software and then click Download. Install the software Double-click SampleTrackingUtility_setup.exe and follow the instructions to install the software. By default the software is installed to C:\Program Files\Applied Biosytems\Sample Tracking Utility. 3 Start the software Double-click the OpenArray Sample Tracker Software icon on the desktop. QuantStudio 12K Flex Software version 1. Open the QuantStudio 12K Flex Software. 2. From the Home screen, go to the Tools pane, then click OpenArray Sample Tracker Software. The OpenArray Sample Tracker Software opens in a new window. 5
(Optional) Set preferences Set preferences for your default experiment type, OpenArray plate format, and import and export directories. 1 Open the Preferences dialog box From the menu bar, select View Preferences to open the Preferences dialog box. 2 Select your Preferences a. From the Experiment Type drop-down list, select from Genotyping, Gene Expression, 3 Sample Fixed Panels, 4 Sample Fixed Panels. b. From the OpenArray Plate drop-down list, select an OpenArray plate format. c. From the Pipettor drop-down list, select Fixed or Adjustable as the Pipettor type. d. From the Import Data Directory, browse and save a directory. The Sample Tracker import data directory; the OpenArray Sample Tracker Software will automatically open this directory when you import *.csv files. e. From the Export Data Directory, browse and save a directory. The Sample Tracker export data directory; when you export *.csv or *.xls files the OpenArray Sample Tracker Software will automatically save the files in this directory. f. Click Save. 6
Enter experiment properties In the Sample Tracker Software Properties window, enter general information about your experiment. Figure 1 Properties window (the numbers in the screen capture refer to the step numbers in this procedure) step 2 step 3 step 4 step 5 1 Open the Properties window In the Sample Tracker navigation pane, click Properties (default view). 2 3 Select the experiment type Select the OpenArray plate format From the Experiment Type drop-down list, select the appropriate experiment type: Genotyping Gene Expression (also referred to as real-time PCR experiments) 3 Sample Fixed Panels 4 Sample Fixed Panels From the OpenArray Plate drop-down list, select the OpenArray plate format: If the experiment type is... Then select one of the following formats... Genotyping Genotyping 16 Genotyping 32 Genotyping 64 Genotyping 128 Genotyping 192 Genotyping 256 Gene Expression (real-time PCR) Gene Expression 18 Gene Expression 56 Gene Expression 112 Gene Expression 168 Gene Expression 224 3 Sample Fixed Panels N/A 4 Sample Fixed Panels N/A N/A = Not applicable 7
4 5 Select the type of pipettor (Optional) Enter the 384- well sample plate serial number From the Pipettor drop-down list, select Fixed or Adjustable. If you have added a serial number or barcode to the OpenArray 384-Well Sample Plate, enter the serial number. 8
Enter sample information for the 96-well reaction plates In the Sample Tracker Software Samples window, enter the sample information for the 96-well reaction plates. 1 Open the Samples window In the Sample Tracker navigation pane, click Samples. 2 Enter the sample information You can enter sample information either manually or by importing *.csv files. Import sample information 1. In a simple text program or spreadsheet program, create one or more *.csv files, one for each 96-well reaction plate. For detailed instructions, see Create *.csv files on page 21. 2. In the Sample Tracker Software Samples window, select the appropriate tab for the 96-well reaction plate (96-Well Plate n). Note: The number of plate tabs displayed in the Samples window depends on the OpenArray plate format that you selected in the Properties window. See Select the OpenArray plate format on page 7. 3. Click Import, then browse to and open the appropriate *.csv file for the selected plate tab. The sample information is displayed in the Sample Tracker Software. Note: All sample information is displayed in the table view; only the sample ID is displayed in the plate layout view. Manually enter sample information 1. In the Sample Tracker Software Samples window, select the appropriate tab for the 96-well reaction plate (96-Well Plate n). Note: The number of plate tabs displayed in the Samples window depends on the OpenArray plate format that you selected in the Properties window. See Select the OpenArray plate format on page 7. 2. Click View Table. 3. Enter sample IDs: Double-click inside the SampleInfo.SampleID table cell to activate it, then enter identifying information for the sample. From a spreadsheet containing sample names, copy one or more cells, click-drag in the table to select rows, and then enter Ctrl-V to paste the names. 9
3 Review the sample information Review the sample information for accuracy, and edit the information if needed. The following table describes the actions you can perform in the Samples window. View Step Action Plate Layout a To toggle between the plate layout and table views, click View Table or click View Plate Layout. b To zoom in on the wells, click Zoom In. c To zoom out from the wells, click Zoom Out. d To fit all wells into the default plate layout size, click Fit to Size. e To import sample information from a *.csv file, click Import. f To delete selected sample information, select one or more cells, then click Clear. To delete all sample information, do not select any cells and click Clear. IMPORTANT! The Clear function permanently deletes the sample information. There is no Undo function. g To edit the sample ID, double-click a well in the plate layout to activate the well, then type over the existing text. b c d e f a g Table h To toggle between the plate layout and table views, click View Table or click View Plate Layout. i To import sample information from a *.csv file, click Import. j To delete selected sample information, select one or more cells, then click Clear. k To delete all sample information, do not select any cells and click Clear. IMPORTANT! The Clear function permanently deletes the sample information. There is no Undo function. To edit the sample ID: Double-click the SampleInfo.SampleID cell to activate it, then type over the existing text. From a spreadsheet containing sample names, copy one or more cells, click-drag in the table to select rows, and then enter Ctrl-V to paste the names. Note: To paste all the selected samples, you must select the same amount of copied cells and then paste. i j k h 10
View the sample mapping In the Sample Tracker Software Sample Mapping window, you can view the sample mapping from plate to plate: 384-Well Plate tab Displays the sample mapping from 96-well reaction plates to the 384-well sample plates (this page) OpenArray tab Displays the sample mapping from 384-well sample plates to the OpenArray plates (page 13) 384-Well Plate tab The 384-Well Plate tab displays the sample mapping from 96-well reaction plates to 384-well sample plates. 1 Open the Sample Mapping window a. In the Sample Tracker navigation pane, click Sample Mapping. b. Click the 384-Well Plate tab (default view). 2 Select the plates to view a. From the Show drop-down list, select the plates to view: 96-well reaction plates (96-Well Plate n) and/or 384-well sample plate (384-Well Plate). Note: The number of plates displayed in the Show drop-down list depends on the OpenArray plate format that you selected in the Properties window. See Select the OpenArray plate format on page 7. b. (Optional) Move the samples from one of the 96-well reaction plates to another: 1. Click Swap. 2. Select a plate, click (Up) or (Down) to change the plate position, then click OK. 11
3 Review the sample information The samples are reassigned to each plate based on the order of the plates. c. (Optional) For some OpenArray Plate Formats, only half of the samples from the 96-well plate are loaded per instrument run. To view the plates for the second run, click. Note: For some OpenArray Plate Formats, use the 12-channel pipette to vertically load samples into columns. Review the sample information for accuracy. The following table describes the actions you can perform in the 384-Well Plate tab of the Sample Mapping window. Note: You cannot edit the sample information in the Sample Mapping window. View Step Action Plate Layout a To toggle between the plate layout and table views, click View Table or click View Plate Layout. b To zoom in on the wells, click Zoom In. c To zoom out from the wells, click Zoom Out. d To fit all wells into the default plate layout size, click Fit to Size. e To enable using the lower half or the right side of the 384-Well Plate, click. f To enable using the upper half or the left side of the 384-Well Plate, click. a b c d 12
View Step Action Table e To toggle between the plate layout and table views, click View Table or click View Plate Layout. e OpenArray tab The OpenArray tab displays the sample mapping from the 384-well sample plate to the OpenArray plates. 1 Open the Sample Mapping window a. In the Sample Tracker navigation pane, click Sample Mapping. b. Click the OpenArray tab. 2 Select the plates to view From the Show drop-down list, select the OpenArray plates to view (Plate n). 13
3 Review the sample information Review the sample information for accuracy. The following table describes the actions you can perform in the OpenArray tab of the Sample Mapping window. Note: You cannot edit the sample information in the Sample Mapping window. View Step Action Plate Layout a To zoom in on the wells, click Zoom In. b To zoom out from the wells, click Zoom Out. c To fit all wells into the default plate layout size, click Fit to Size. a b c 14
Print or export data In the Sample Tracker Software Sample Mapping window, you can print or export data using the following functions: Print PDF button Prints data to *.pdf files; you can use the printed *.pdf files to guide your sample pipetting (this page) Export button Exports data in one of two formats: Export *.csv (in table format) Exports data as *.csv files; you can import the sample information from these *.csv files into the OpenArray AccuFill System Software to create an integrated *spf or *tpf or into the QuantStudio 12K Flex Software (page 16) Export Excel (in plate layout format) Exports data as Microsoft Excel Software (*.xls) files; you can use the exported *.xls files as a pipetting guide (page 18) Print *.pdf Plate Report files 1 Open the Sample Mapping window a. In the Sample Tracker navigation pane, click Sample Mapping. b. Click the 384-Well Plate tab (default view). 2 Select the plates to print a. Click Print PDF. b. Select the plates to print: 96-well reaction plates (96-Well Plate n) and/or 384-well sample plate (384-Well Plate (for AccuFill)). Note: The number of plates displayed in the dialog box depends on the OpenArray plate format that you selected in the Properties window. See Select the OpenArray plate format on page 7. 15
2 Select the plates to print (continued) c. Click OK. The Sample Tracker Software displays the Plate Report window. 3 View, print, and/or save the Plate Report Use the tools in the Plate Report window to view, print, and/or save the report, then close the Plate Report window. Save Print Browse pages Size Export *.csv files in table format 1 Open the Sample Mapping window a. In the Sample Tracker navigation pane, click Sample Mapping. b. Click the 384-Well Plate tab (default view). 16
2 Select the plates to export a. Click Export Export *.csv. b. Select the plates to export: 96-well reaction plates (96-Well Plate n), 384-well sample plate (384-Well Plate), and/or OpenArray plates (OpenArray Plate n). Note: The number of plates displayed in the dialog box depends on the OpenArray plate format that you selected in the Properties window. See Select the OpenArray plate format on page 7. c. Enter a file name prefix in the Export Directory field. The Sample Tracker Software automatically assigns the file names using the file name prefix. d. Click OK; click OK again to close the Data exported successfully message. All plates are saved to individual *.csv files in the export directory you selected in the Preferences dialog box. 3 (Optional) Open/review exported *.csv files Double-click an exported file to open it in Microsoft Excel Software. 17
4 (Optional) Import *.csv files into other applications Import the exported files into other applications: 96-Well Plate files Use these files as needed for your own record keeping. 384-Well Plate file Use this file with the OpenArray AccuFill System Software to create an integrated *.spf or *.tpf file. containing sample names. OpenArray Plate file Use this file to import setup information directly into the QuantStudio 12K Flex Software or to add sample information after the data has been acquired. Export *.xls files in plate layout format 1 Open the Sample Mapping window a. In the Sample Tracker navigation pane, click Sample Mapping. b. Click the 384-Well Plate tab (default view). 2 Select the plates to export a. Click Export Export Excel. b. Select the plates to export: 96-well reaction plates (96-well Plate n), 384-well sample plate (384-Well Plate), and/or OpenArray plates (OpenArray Plate n). 18
Note: The number of plates displayed in the dialog box depends on the OpenArray plate format that you selected in the Properties window. See Select the OpenArray plate format on page 7. c. Browse to an export directory, enter a file name, then click Save. Note: All plates are saved to one *.xls file in the export directory. d. Click OK to close the Data exported successfully message. 3 (Optional) Open/review the exported *.xls file Double-click the exported file to open it in Microsoft Excel Software. 19
Close the software IMPORTANT! Sample Tracker Software does not save the sample information in any of the windows. When you close the software, all sample information is lost. To save the sample information, export or print the data before closing; see Print or export data on page 15. From the menu bar, select File Exit, then click OK to close the Sample Tracker Software:. 20
Create *.csv files If you are entering sample information into the Samples window by importing *.csv files, use a template file (installed with the software) to create the *.csv files as described in this section. Note: Create a separate *.csv file for each 96-well reaction plate. 1 2 Open the template file Open the file 96-Well Sample Plate x.csv template file, where x corresponds one of your 96-well plates, in a simple text program or in a spreadsheet program (such as Microsoft Excel Software). By default, the template files are installed to C:\Program Files\Applied Biosytems\Sample Tracking Utility\examples. Enter the sample name Follow these guidelines: Include all samples and all No Template Controls (NTCs). Enter information for only one sample or NTC per row. a. In the SampleInfo.SampleID column, enter the sample name for each sample in the 96-well reaction plate. b. (Optional) In the SampleInfo.SampleDescription column, enter the sample description. Valid characters include spaces, numbers, letters, and punctuation. Leave all the other columns empty. Note: For each *.csv file, you can have a maximum of 97 rows: one row for the column headings, and up to 96 rows with sample information. All extra rows are ignored. 3 Save the file Save the spreadsheet as a *.csv file: a. Select File Save As. b. Browse to a save location, enter a file name, then select *.csv as the file type. Note: We recommend that you name the file with the same unique identifier as the 96-well reaction plate. c. Click Save. d. At the prompt, click OK to save only the active sheet. e. If you are prompted to keep the workbook in the current format (*.csv), click Yes. 21
For Research Use Only. Not intended for human or animal therapeutic or diagnostic use. LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) DISCLAIM ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT. TO THE EXTENT ALLOWED BY LAW, IN NO EVENT SHALL LIFE TECHNOLOGIES AND/ OR ITS AFFILIATE(S) BE LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF. 2012 Life Technologies Corporation. All rights reserved. The trademarks mentioned herein are the property of Life Technologies Corporation or their respective owners. Excel and Microsoft are registered trademarks of Microsoft Corporation. TaqMan is a registered trademark of Roche Molecular Systems, Inc., used under permission and license. Headquarters 5791 Van Allen Way Carlsbad, CA 92008 USA Phone +1 760 603 7200 Toll Free in USA 800 955 6288 For support visit www.lifetechnologies.com/support www.lifetechnologies.com