Thermo Scientific Ion S5 User Manual
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Thermo Scientific Ion S5 User Manual

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™
Ion 520
& Ion 530
USER GUIDE
for use with:
Ion Chef
™
System
™
Ion S5
System
Ion S5
™
XL System
™
Ion GeneStudio
S5 System
Ion GeneStudio
™
S5 Plus System
™
Ion GeneStudio
S5 Prime System
Catalog Number A30670
Publication Number MAN0015805
Revision F.0
For Research Use Only. Not for use in diagnostic procedures.
™
ExT Kit – Chef

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Summary of Contents for Thermo Scientific Ion S5

  • Page 1 ™ ™ Ion 520 & Ion 530 ExT Kit – Chef USER GUIDE for use with: Ion Chef ™ System ™ Ion S5 System Ion S5 ™ XL System ™ Ion GeneStudio S5 System Ion GeneStudio ™ S5 Plus System ™...
  • Page 2 (see “Perform an instrument reset run with an initialized sequencer that is loaded with an unused Reagents cartridge” on page • Web links updated 13 October 2016 New user guide with detailed instructions for use of the Ion 520 ™ & Ion 530 ™ ExT Kit – ™...

  • Page 3: Table Of Contents

    Planned Run workflow key fields ..........22 Ion 520 ™...
  • Page 4 Start the cleaning ............58 Ion 520 ™...
  • Page 5 Limited product warranty ............76 Ion 520 ™...

  • Page 6: Chapter 1 Product Information

    XL Sequencer, or Ion GeneStudio S5 Series Sequencer. ™ ™ The Ion Chef Instrument uses automated isothermal amplification technology with the Ion 520 & ™ Ion 530 ExT Kit – Chef to prepare 400 to 600‑base‑read templates with greatly reduced run times compared to emulsion PCR-based templating.

  • Page 7: Software Compatibility

    ExT Kit – Chef contains all the supplies that are required to prepare and ™ ™ ™ sequence 4 Ion 520 Chips or Ion 530 Chips. Cat. No. A30670 supports 4 single-chip Ion Chef runs and 4 sequencer initializations (1 sequencing run/sequencer initialization) for 400 to 600‑base‑read libraries.

  • Page 8: Related Products

    Related products Compatible Ion Chip ™ kits ™ ™ ™ The following Ion Chip kits, ordered separately, are compatible with the Ion 520 & Ion 530 ExT Kit – Chef. Description Cat. No. Quantity Storage ™...

  • Page 9: Ion S5 ™ Controls Kit Plus

    For laboratories that experience frequent power outages or line voltage fluctuations, we recommend that you use an uninterruptible power supply that is compatible with 2500 W output or higher. Ion 520 ™ & Ion 530 ™...

  • Page 10: About The Ion Chef ™ System

    XL Sequencer, or Ion GeneStudio Series Sequencer. The system uses a set of cartridge-based consumables and reagents that enables ™ ™ a user to load an Ion 520 Chip, or an Ion 530 Chip in about 7 hours with less than 15 minutes ™...

  • Page 11: Interior Hardware And Consumables

    ISPs. Chip-loading centrifuge – Performs centrifugation of the sequencing chip that has been mounted to a chip-loading adapter and loaded with template-positive ISPs, and a chip balance loaded opposite to the sequencing chip. Ion 520 ™ & Ion 530 ™...

  • Page 12: About The Ion Chef ™ System Touchscreen Interface

    • Torrent Server: add and manage Ion Torrent Server connections • Clean Ion Chef: proceed directly to the instrument cleaning routine • Check for updates: check availability of system software updates Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 13: Workflow

    Chapter 1 Product information Workflow Workflow ™ ™ The following workflow illustrates how to prepare and a load sample using the Ion 520 & Ion 530 ™ ™ ™ Kit – Chef, and Ion Chef System for sequencing on an Ion S5...

  • Page 14: Chapter 2 Before You Begin

    WARNING! The protection that is provided by the equipment can be impaired if the instrument is operated outside the environment and use specifications, the user provides inadequate maintenance, or the equipment is used in a manner that is not specified by the manufacturer (Thermo Fisher Scientific). Ion 520 ™ & Ion 530 ™...

  • Page 15: Guidelines For Using Ion Chef ™ Consumables And Reagents

    Before loading consumables into the instrument, wipe the compartments dry with a laboratory wipe or absorbent cloth, if needed. ™ • Thaw the Ion S5 ExT Chef Reagents cartridge at room temperature for 45 minutes before use. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...
  • Page 16 Note: If the instrument is not connected, see the Ion Chef Instrument Network Connection User Guide (Pub. No. MAN0013444) for instructions on how to configure a direct or indirect network connection. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 17: Chapter 3 Create A Planned Run

    ™ a complete description of each field in the Create Plan workflow bar, see the Torrent Suite Software Help, available by clicking the Help button in the software. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 18: Create A Planned Run

    (Optional) For barcoded libraries, select the barcode set used during library preparation from the Barcode Set dropdown list. e. Select IonChef for Template Kit, then select Ion 520 & Ion 530 ExT Kit-Chef from the Template Kit dropdown list.
  • Page 19 5. Review the Plugins and Projects screens, then make selections appropriate to your run. 6. In the Plan step, enter or make the following selections: a. Enter a Run Plan Name, then select Reference and BED files appropriate to your run. Ion 520 ™ & Ion 530 ™...
  • Page 20 Scan or enter the barcode of the Ion Chef Library Sample Tube into the Sample Tube Label field. d. Scan or enter the chip barcode into the Chip Barcode field. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...
  • Page 21 The run is listed on the Planned Runs screen under the name that you specified, and is automatically ™ used by the Ion Chef System when the associated sample is loaded. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 22: Planned Run Workflow Key Fields

    ™ Chip. Library Kit Type Select the kit used to prepare the library. Template Kit Select Ion 520 & Ion 530 ExT Kit-Chef. Sequencing Kit Select Ion S5 ExT Sequencing Kit. Barcode Set (optional) If you are using barcodes with: •...
  • Page 23 Set thresholds for Bead Loading, Usable Sequence, and Key Signal. In the Torrent ™ Suite Software Monitor4Runs in Progress screen, an alert is displayed if the values for a run fall below the selected thresholds. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 24: Start The Ion Chef

    ™ • Start an Ion Chef • Unload the chips for sequencing Materials required ™ ™ • Ion 520 & Ion 530 ExT Kit – Chef (Cat. No. A30670) • Ion 520 ™ ™ Chip or Ion 530 Chip •...

  • Page 25: Guidelines For Library Dilution

    Ion PGM Template IA 500 Kit may need to re-optimize library ™ ™ concentration for the Ion 520 & Ion 530 ExT Kit – Chef. • Recommendations are based on qPCR quantification. If libraries are quantified with an Agilent ™...

  • Page 26: Add The Diluted Libraries To The Ion Chef

    2. Cap and store the diluted DNA library on ice, or at 4°C, until you are ready to load the tube into the ™ Reagents cartridge and the Ion Chef Instrument. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 27: System

    ™ ™ · Use only the materials supplied in the Ion 520 & Ion 530 ExT Kit – Chef to run the centrifuges at the rated speeds. Do not remove or change the rotors. Inspect the buckets before each use to assure normal operation.

  • Page 28: Load The Tip Racks And Pcr Plate

    Two Ion Chef Piercing Tips are pre-loaded into tip positions G7 and H7 on the Ion S5 ExT Tip Cartridge. · Keep the cover for later use. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 29: Load The Reagents And Solutions Cartridges

    ™ ExT Chef Reagents cartridge on the bench to force the reagents to the bottoms of the tubes. 2. If bubbles are present below the surface of the liquid, repeat step 1. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...
  • Page 30 Ensure that all four tubes are uncapped. 6. Gently tap the Ion S5 ™ Chef Solutions cartridge on the bench to force the reagents to the bottoms of the tubes. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 31: Load The Recovery Tubes And Enrichment Cartridge V2

    2. Place a Recovery Station Disposable Lid v2 over each centrifuge by lining up the tab with the depression on the deck, then snap into place. Ensure that the lids snap completely into place by applying firm downward pressure along the lid perimeter. Ion 520 ™ & Ion 530 ™...
  • Page 32 IMPORTANT! Ensure that the Enrichment Cartridge v2 is loaded so that the lettering on the cartridge is right‑side‑up. 11 12 Enrichment station Lettering Enrichment Cartridge v2 Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 33: Load The Chip-Loading Centrifuge

    The chip loaded in Position 1 is loaded with ISPs prepared from the DNA library in the Library Sample Tube loaded in Position A of the Reagents cartridge. Ion 520 ™ & Ion 530 ™...
  • Page 34 90° outwards when touched. Then close the lid of the Chip-loading centrifuge. IMPORTANT! Do not obstruct or place any object on top of the lid. Ion 520 ™ & Ion 530 ™...

  • Page 35: Confirm That Consumables Are Correctly Installed

    ™ are installed correctly to the deck before you start a run. The Ion Chef Instrument does not verify all aspects of the consumable setup before beginning each run. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 36: Pre-Run Checklist

    Chapter 4 Start the Ion Chef ™ ™ Load the Ion Chef System ™ Ion Chef pre-run checklist 11 12 Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 37: Run

    If you selected Quick Start, proceed to step 5, otherwise proceed to step 4. 4. (Step by step setup only) In the Run Options screen, tap Prepare Chip to select the templating run option. Ion 520 ™ & Ion 530 ™...
  • Page 38 Instrument before starting a run. To ensure proper and safe instrument operation, ensure that all consumables are installed correctly before you continue. 7. When the Deck Scan is complete, tap Next to display the Data Destination screen. Ion 520 ™ & Ion 530 ™...
  • Page 39 Pause chip loading step: An additional 1 hour is required for chip loading to complete the run. Total run time is longer because an extra centrifugation step is required with the Pause option. Ion 520 ™ & Ion 530 ™...
  • Page 40 ™ when prompted to do so by the Ion Chef Instrument (approximately 5.75 hours into the run). a. When prompted to remove the QC sample, open the instrument door. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...
  • Page 41 Note: If you cannot sequence a loaded chip immediately, place the chip into a separate chip storage container and store at 4°C until you are ready to sequence it (up to 6–8 hours maximum). Ion 520 ™ & Ion 530 ™...

  • Page 42: Unload The Chip For Sequencing

    Chip Balance Remove the adapter/chip/bucket assembly 3. Unload the chip from the adapter/chip/bucket assembly. a. Apply pressure to both ends of the Chip Adapter, then remove and discard the Chip Adapter. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...
  • Page 43 Ensure that both sides of the door are locked after closing it. Lift door first Press down to lock Lower Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...
  • Page 44 If you choose to store a loaded chip, remove the chip from 4°C storage (but keep it in the storage container) at least 20 minutes before running it, allowing the chip to warm to room temperature. Ion 520 ™ & Ion 530 ™...

  • Page 45: Initialize The Sequencer

    ExT Wash Solution bottle. Waste reservoir located behind the Ion S5 ExT Wash Solution bottle (shown on the right). ™ Ion S5 Cleaning Solution bottle Waste reservoir Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 46: Before You Begin

    An instrument reset run is required before reinitialization. For more information, see “Perform an instrument reset run with an initialized sequencer that is loaded with an unused Reagents cartridge” on page Ion 520 ™ & Ion 530 ™...

  • Page 47: Initialize The Sequencer

    ExT Wash Solution bottle is thoroughly mixed. Then remove the red cap and install. 6. Ensure that the used sequencing chip from the previous run is properly seated in the chip clamp and the chip clamp is pushed in all the way. Ion 520 ™ & Ion 530 ™...
  • Page 48 9. When initialization is complete (~50 minutes), tap Home. The instrument is now ready for a sequencing run. For information on recycling and disposal of used components, see “Reagent consumables disposal” on page Ion 520 ™ & Ion 530 ™...

  • Page 49: Chapter 6 Start The Sequencing Run

    If your Planned Run does not advance to the "Planned" status in Torrent ™ ™ Suite Software after successful completion of an Ion Chef run, see “Planned Run status does not advance to "Planned"” on page Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...
  • Page 50 4. Confirm that the correct Planned Run has auto-populated, then tap Review. Note: Ensure the Enable post-run clean checkbox is selected so that the post-run cleaning is performed automatically. Ion 520 ™ & Ion 530 ™...
  • Page 51 When the sequencing run is complete, the instrument automatically performs the cleaning procedure unless the Post-Run/Clean checkbox was deselected. After cleaning, the touchscreen ™ returns to the main menu. Review the results with Torrent Suite Software. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 52: Maintain The Sequencer

    2. Wearing gloves, insert the Ion S5 ™ Cartridge Tool firmly into the CO scrubber until the flange stops on the top of the cartridge. Ion S5 ™ Cartridge Tool Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 53: Recycle Ion S5

    3. Rinse the empty bottle with water. Pour out the rinse water into the same liquid waste receptacle. 4. Recycle or dispose of the clean bottle, cap, sipper, and filter according to applicable regulations. Ion 520 ™ & Ion 530 ™...

  • Page 54: About The Cleaning Protocol

    ™ IMPORTANT! Clean the Ion Chef Instrument as described in the following pages after every run. To prevent contamination, do not operate the instrument unless it has been recently cleaned. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 55: Remove And Dispose Of Used Consumables

    2. Lift the instrument door to the top of the travel until the latch mechanism engages. Hold here, then lift 3. Remove, then discard the PCR Plate from the thermal cycler sample block. Ion 520 ™ & Ion 530 ™...
  • Page 56 • Recovery Station Disposable Lid v2 • Recovery Tubes v2 8. Remove the Chip Balance from the Chip-loading centrifuge. Do not discard. 9. Close the Chip-loading centrifuge lid. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 57: Inspect And Clean The Recovery Centrifuges And Buckets

    4. Use lint-free wipes treated with 70% isopropanol to clean the following parts. • Inside rim of the centrifuge. • Bottom of the centrifuge bowl. • Outside and inside of the centrifuge buckets. Ion 520 ™ & Ion 530 ™...

  • Page 58: Start The Cleaning

    ™ Instrument touchscreen that appears after run completion. Note: You can also clean the instrument at any time starting from the home touchscreen. Tap Settings4Clean Ion Chef. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...
  • Page 59 Instrument emits UV light at 254 nm. Wear appropriate eye wear, protective clothing, and gloves when working near the instrument. Do not look directly at the UV light while it is illuminated during the cleaning routine. Ion 520 ™ & Ion 530 ™...

  • Page 60: Appendix A Troubleshooting

    ™ operation, a noticeable coating the Ion Chef Instrument” on page of liquid can collect on the bowl and buckets of the Recovery centrifuge following repeated runs. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...
  • Page 61 Technical Support. If possible, capture an image of the alert or error message to help troubleshoot. IMPORTANT! The detected problem might impact the performance of the sequencing run. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...
  • Page 62 2. In the Plan tab, click Planned Runs. remains listed as "Reserved" in 3. For the Planned Run of interest, click Torrent Suite ™ Software. 4Completed on Chef. The status changes to "Planned". Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 63: Ion S5 /Ion Genestudio ™ S5 Systems Setup And Operation

    • If the red "Alarms" and/or "Events" message still appears in the main menu, contact Technical Support. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 64: Initialization-General Errors

    1. Finger-tighten the bottles. 2. If the bottle continues to leak, replace the • Bottle was damaged or bottle. defective. 3. If leak check continues to fail, contact Technical Support. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 65: Appendix B Supplemental Procedures

    IMPORTANT! Perform the cleaning with a used reagent cartridge and wash solution bottle installed. The cleaning procedure pumps cleaning solution into the wash solution bottle and reagent cartridge making them unsuitable for sequencing. Ion 520 ™ & Ion 530 ™...

  • Page 66: Perform An Instrument Reset Run With An Initialized Sequencer That Is Loaded With An Unused Reagents Cartridge

    5. In the Select Run screen, tap Edit, then in the Detail screen set the number of flows to 200. Ensure that the Post-Run/Clean checkbox is selected, then tap Close. 6. Tap Start run, then tap Accept to confirm that Post-Run Clean is enabled, and to start the run. Ion 520 ™ & Ion 530 ™...

  • Page 67: Quality Control Of Ion Sphere ™ Particles

    ™ Note: You must install the Ion Chef Instrument firmware update in Torrent Suite Software 5.12 or later to access the XYƟ calibration and Z calibration routines. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 68: Appendix C Safety

    • WARNING! – Indicates a potentially hazardous situation that, if not avoided, could result in death or serious injury. • DANGER! – Indicates an imminently hazardous situation that, if not avoided, will result in death or serious injury. Ion 520 ™ & Ion 530 ™...

  • Page 69: Conformity Symbols

    Indicates conformity with safety requirements for Canada and U.S.A. Indicates conformity with European Union Low Voltage Directive 2006/95/EC, EMC Directive 2014/30/EU, and R&TTE Directive 1999/5/EC. Indicates conformity with Australian standards for electromagnetic compatibility. Ion 520 ™ & Ion 530 ™...

  • Page 70: Location Of Safety Labels On This Instrument

    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. Ion 520 ™ & Ion 530 ™...

  • Page 71: Electrical Safety

    UV lamp is not powered when the door is open. Safety and electromagnetic compatibility (EMC) standards The instrument design and manufacture complies with the following standards and requirements for safety and electromagnetic compatibility. Ion 520 ™ & Ion 530 ™...

  • Page 72: Safety Compliance

    Directive 2012/19/EU European Union “WEEE Directive” – Waste electrical and electronic equipment Directive 2011/65/EU European Union “RoHS Directive” – Restriction of hazardous substances in electrical and electronic equipment Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 73: Instrument Safety - Ion S5

    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. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 74: Biological Hazard Safety

    Laboratories (BMBL), 5th Edition, HHS Publication No. (CDC) 21-1112, Revised December 2009; found at: https://www.cdc.gov/labs/pdf/CDC-BiosafetymicrobiologicalBiomedicalLaboratories-2020- P.pdf · World Health Organization, Laboratory Biosafety Manual, 3rd Edition, WHO/CDS/CSR/LYO/2004.11; found at: www.who.int/publications/i/item/9789240011311 Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 75: Documentation And Support

    Particles Quality Assessment for the Ion Proton and Ion S5 Systems Using MAN0007496 ™ the Guava easyCyte 5 Benchtop Flow Cytometer User Bulletin Note: For additional documentation, see “Customer and technical support”. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...

  • Page 76: Customer And Technical Support

    Life Technologies Corporation and/or its affiliate(s) warrant their products as set forth in the Life Technologies' General Terms and Conditions of Sale at www.thermofisher.com/us/en/home/ global/terms-and-conditions.html. If you have any questions, please contact Life Technologies at www.thermofisher.com/support. Ion 520 ™ & Ion 530 ™ ExT Kit − Chef User Guide...
  • Page 78 Ion 520 & Ion 530 ExT Kit - Chef_UG_MAN0015805-v9-GUID-3C5C5686-4A0C-47E8-A6B5- CC17DB083BA8-2021/11/17 18:24:55 en 18:18:33.259Z thermofisher.com/support | thermofisher.com/askaquestion thermofisher.com 24 November 2021...

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