Search
Search
查看更多产品信息 Ion PGM™ Template OT2 200 Kit - FAQs (4480974)
28 个常见问题解答
The "time remaining" is not entirely accurate. The centrifuge may keep rotating for about 15 minutes after the time has become 0:00. If it rotates for more than 15 minutes, please contact Technical Support.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
The pressure inside the instrument may be above normal. If the Ion OneTouch 2 firmware is older than v540, please update it to the latest version.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
No, you may not. Please exchange the oil when switching between different kits. Contact Technical Support for any needed assistance when switching kits.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
It may be rubber from the packing. The amount varies among instruments and it is not anything to be concerned about, as it will be removed by the Ion OneTouch ES.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
The pH of W1 may be out of range or the volume of W1 may be too small or there may have been a minor problem during measurement. Check the amount of W1, press the 'Start' button on the screen, and restart the measurement. If it passes, continue to start the run. If an error appears again, please note the pH of W1, the amount of W1, as well as the error message, and contact Technical Support.br/>
Please note that passing pH values for the reagents may vary depending on the sequencing kit used, but the instrument will automatically determine the correct pH range depending on the sequencing kit selected during initialization. If you are performing the reagent check outside of the initialization, please contact Technical Support for guidance.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Firmware updates to the software controlling the Ion OneTouch 2 Instrument are periodically released. To update the firmware to the appropriate version, use either a USB flash drive or an ethernet connection, as described on page 11 of the Ion OneTouch 2 System - Installation, Setup, and Maintenance User Guide (http://tools.thermofisher.com/content/sfs/manuals/MAN0014388_IonOneTouch2Sys_UG.pdf ).
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
We recommend removing the samples from the Ion OneTouch 2 instrument ≤ 16 hours after starting the run. After centrifuging and removing the samples from the instrument, follow the ISP collection protocol to recommended stopping points and follow the instructions for preparing the unenriched ISPs for storage. The ISP suspension can be stored at 2 degrees C to 8 degrees C for up to 3 days.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
In a typical Ion OneTouch 2 run, you should expect ~18 mm drop in the level of oil in the tube (~22 mL consumed), and ~13 mm drop in the recovery solution (~15 mL consumed). During cleaning, you should expect to collect ~10 mL of oil in the 50 mL conical waste collection tube.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Due to differences in reagent formulations between kit types, we recommend following the Demonstrated Protocol: How to Set Up the Ion OneTouch 2 Instrument When Switching Between the Ion PGM System and Ion Proton System (http://ioncommunity.thermofisher.com/docs/DOC-7265) if using more than one Ion OneTouch 2 Template kit type on your instrument. Briefly, the instrument lines must be primed with the new kit reagents by running a cleaning and initialization procedure prior to setting up the next run. Please see the above user guide for detailed instructions.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
The input amount for template preparation on the Ion OneTouch 2 is library type specific. Occasionally, library input titration may be required to optimize templated ISP clonality and maximize sequencing throughput. Please see the specific guidelines for your library type in the appropriate library preparation user guide that can be found here: http://www.thermofisher.com/us/en/home/technical-resources/technical-reference-library/next-generation-sequencing-support-center/ngs-library-preparation-support.html
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
For the Ion PGM System, we offer:
- Ion PGM Hi-Q View OT2 Kit (Cat. No. A29900) for template preparation of libraries up to 400 bp in length.
For the Ion Proton System, we offer:
- Ion PI Hi-Q OT2 200 Kit (Cat. No. A26434) for template preparation of libraries up to 200 bp in length.
For the Ion S5 System and Ion S5 XL System, we offer two kits:
- Ion 520/530 Kit-OT2 (Cat. No. A27751) for template preparation of libraries up to 400 bp in length.
- Ion 540 Kit- OT2 (Cat. No. A27753) for template preparation of libraries up to 200 bp in length.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Currently, the Ion PGM System supports up to 400–base reads.
For up to 400-base reads, using the Ion PGM Hi-Q View Chemistry and Ion PGM One Touch 2 system, we recommend:
• Ion PGM Hi-Q View One Touch 2 Kit (Cat. No. A29900)
• Ion PGM Hi-Q View Sequencing Kit (Cat. No. A30044)
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Signal Processing Input - Required to reanalyze an Ion Torrent Ion PGM or Ion Torrent Ion Proton run from scratch. (The Output file category is also required).
Basecalling Input - Required to re-analyze an Ion PGM or Ion Proton run from basecalling. (The Output file category is also required).
Output - Required to see the run report in the Torrent Browser and either to reanalyze the run or to launch a plugin.
Intermediate - Useful to troubleshoot a run. Not required for the run report or for re-analysis.
Intermediate files can be deleted if not needed for run troubleshooting. Depending on your institution, you may need to keep all other files (Signal Processing, Basecalling, and Output).
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Follow these steps to change the DNA barcode ID:
- Open a run reports listing in the “Data,” “Completed Runs & Reports” tab.
- In the list view, click the “Edit” button on the right side of the run listing. The Edit Run window opens.
- Click the barcode menu pull-down and choose the correct barcode set. If you have custom barcode sets, your list is different. Click the “Save” button (in the bottom right corner).
- You can now reanalyze the run from the “Data,” “Completed Runs & Reports” tab.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Log in to Torrent Browser and click the “Data” tab, “Completed Runs & Reports page”, and find your run name. In the table view, click the “Reanalyze” option in the gear menu on the right of the run entry. The main run analysis dialog opens. Click the “Advanced” button to display the additional run parameter options. Click the “Alignment Reference” pull-down menu and select the reference for this run. (Optional) Change other advanced options if required. (See “Work with Completed Runs” for a description of the advanced fields.) Click the “Start Analysis” button.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
The GGCCAAGGCG sequence is part of the RNA library adapter sequence. This sequence can be automatically trimmed by the software by selecting the “RNA_Barcode_None” option under the Barcodes menu. The run can be reanalyzed with the correct barcode settings to trim the adapter sequence. In the future, the “RNA_Barcode_None” option should be selected in the run plan or selected on the instrument prior to starting the sequencing run.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Please refer to the Data Management section of the Torrent Suite Software user guide for your version of software. The user guides can be found here under Documents: https://www.thermofisher.com/us/en/home/technical-resources/technical-reference-library/next-generation-sequencing-support-center/ngs-software-support.html
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Primary analysis and secondary analysis of the data is performed by the Ion Torrent Server. Depending on the application, there may be tertiary analysis plugins that can be installed on the Torrent Server. For other applications, such as RNA-Seq, we recommend using third-party software. For more information, please see the Ion NGS Analysis Workflow page (https://www.thermofisher.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-data-analysis-workflow.html).
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
You can find user guides, release notes, and additional information on the Torrent Suite Software here (https://www.thermofisher.com/us/en/home/technical-resources/technical-reference-library/next-generation-sequencing-support-center/ngs-software-support.html).
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
For more information on the informatics workflow and analysis software, such as Ion Reporter and Torrent Suite, please go to the Ion NGS Informatics workflow page (https://www.thermofisher.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-data-analysis-workflow.html).
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Rinse the Proton chip by pipetting 100 µL of isopropanol into the chip, followed by 100 µL of water. This may remove any bubbles or reside from the chip surface that may cause initialization issues.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Open the chip clamp and check for any leaks. If you see solution leaking, please remove the chip and clear the solution with a Kimwipe tissue. DO NOT wipe or scrub, as the socket could be damaged. Clean the socket by gently touching it with a damp Kimwipe tissue. Make sure the socket is dry and replace the chip. Press the “Calibration” button to recalibrate the chip. If it fails again, change the chip to a different one. Also, if you are using an Ion 316 chip v2 on a v3.4 or older instrument, the instrument will not recognize the chip.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
The Ion PGM System and Torrent Server may not be connected. Please shut down the system and server and reboot them. The server may enter a system check after the reboot, which will take 3-4 hours. If you have a monitor and keyboard connected directly to the Torren Server, you can avoid the system check by pressing “c” on the keyboard.
If there is a reason you cannot reboot the system, you can run the Ion PGM System without connection to the server. The runs will be saved inside the system. For 200 bp sequencing, here is the number of runs that may be saved for these chip types:
Ion Torrent Ion 314 chip: 40 runs
Ion Torrent Ion 316 chip: 6 runs
Ion Torrent Ion 318 chip: 5 runs
The data will automatically transfer to the server after connection.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
The pH of the nucleotides may be out of range or there may have been a minor problem during measurement. Press the “Start” button and restart the measurement. If it passes, continue to start the run. If an error appears again, please note the pH of R1, R2, R3, and R4, as well as the error message, and contact Technical Support.
Please note that passing pH values for the reagents may vary depending on the sequencing kit used, but the instrument will automatically determine the correct pH range depending on the sequencing kit selected during initialization. If you are performing the reagent check outside of the initialization, please contact Technical Support for guidance.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Please refer to the “How to assess a PGM sequencing run report” in the Documents section of the NGS Sequencing Support Center (https://www.thermofisher.com/us/en/home/technical-resources/technical-reference-library/next-generation-sequencing-support-center/ngs-support.html).
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Please see the Ion PGM System Product Selection Guide (http://tools.thermofisher.com/content/sfs/brochures/Consumables-Product-Selection-Guide.pdf) for a list of available products for the Ion PGM System workflow organized by application.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
In a typical Ion OneTouch 2 run, you should expect ~18 mm drop in the level of oil in the tube (~22 mL consumed), and ~13 mm drop in the recovery solution (~15 mL consumed). During cleaning, you should expect to collect ~10 mL of oil in the 50 mL conical waste collection tube.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Ion Torrent OneTouch2 protocols can be found at our NGS Support Center (thermofisher.com/ngssupport), in the NGS Template Preparation Support Center section. For all other protocols, please go here (http://www.thermofisher.com/manuals-protocols-search.html).
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.