Thermo Scientific Ion 520 User Manual Download Page 26

Page: 26 / 78

Remove all cartridges and consumables from their packaging, then place them on the bench next
to the Ion Chef

™

Instrument.

Prepare the following cartridges and consumables:

• Chip Adapter and Chip Balance
• Enrichment Cartridge v2
• Ion S5

™

ExT Tip Cartridge

• PCR Plate and Frame Seal v2
• Recovery Station Disposable Lid v2 (2)
• Recovery Tube (12)
• Ion S5

™

Chef Solutions cartridge

• Ion S5

™

ExT Chef Reagents cartridge (from step 1)

IMPORTANT!

Before use, gently tap the Reagents and Solutions cartridges on the bench to force

the reagents to the bottoms of the tubes.

Note:

When stored under normal conditions, a precipitate can form in some tubes of the Ion S5

™

ExT Chef Reagents cartridge. If present, load the cartridge as directed. The precipitate dissolves
when the reagents are mixed during instrument operation.

Add the diluted libraries to the Ion Chef

™

Library Sample

Tube

Pipet 50 µL of the diluted library, or combined library (see “Dilute the sample library”

on page 25

)

into the Ion Chef

™

Library Sample Tube (barcoded tube) from Position A of the Reagents cartridge.

IMPORTANT!

If you are performing a

de novo

sequencing experiment that does not include a

reference BAM file, add 4 μL of the Ion S5

™

ExT Calibration Standard to the diluted library in the

Ion Chef

™

Library Sample Tube. Cap the tube, vortex to mix, then centrifuge for 1–2 seconds to

collect contents at the bottom of the tube.

Note:

If running the

E. coli

DH10B Control 400 Library, or the

E. coli

DH10B Control 600 Library,

dilute the stock library with nuclease-free water following the recommendations in “Dilute the
control library”

on page 25

, then pipet 50 µL of the diluted library into the Ion Chef

™

Library Sample

Tube.

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.

Chapter 4

Start the Ion Chef

™

run

Add the diluted libraries to the Ion Chef

™

Library Sample Tube

Ion 520

™

& Ion 530

™

ExT Kit − Chef User Guide

Summary of Contents for Ion 520

Page 1: ...ures 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 Ion GeneStudio S5 Prime System Catalog Number A30670 Publication Number MAN0015805 Revision F 0 ...

Page 2: ... System maintenance procedures in Ion Chef Instrument User Guide Updated Related documentation to include the Ion Chef Instrument User Guide D 0 12 December 2018 Updated for Ion GeneStudio S5 Series Systems Updated for Torrent Suite Software 5 10 Planned Run creation topics reorganized for ease of use Clarification made to dilute barcoded library pools if used Added a new troubleshooting topic Pla...

Page 3: ...terials not supplied 9 About the Ion Chef System 10 Ion Chef Instrument components 10 Interior hardware and consumables 11 About the Ion Chef System touchscreen interface 12 Workflow 13 CHAPTER 2 Before you begin 14 Precautions 14 Avoid nucleic acid contamination 14 Avoid chip damage 14 Protection by equipment 14 Guidelines for using Ion Chef consumables and reagents 15 Prepare the Ion Chef Instru...

Page 4: ...PTER 5 Initialize the sequencer 45 Ion S5 Ion GeneStudio S5 Systems component positions 45 Before you begin 46 When a manual cleaning of the sequencer is required 46 Initialize the sequencer 47 CHAPTER 6 Start the sequencing run 49 Chip handling guidelines 49 Start the sequencing run 49 Maintain the sequencer 52 Materials required 52 Clean or decontaminate the sequencer 52 Reagent consumables disp...

Page 5: ...ef System 67 APPENDIX C Safety 68 Symbols on this instrument 68 Conformity symbols 69 Location of safety labels on this instrument 70 Safety information for instruments not manufactured by Thermo Fisher Scientific 70 Instrument safety 70 General 70 Physical injury 70 Electrical safety 71 Cleaning and decontamination 71 Ultraviolet UV Safety 71 Safety and electromagnetic compatibility EMC standards...

Page 6: ...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 Each kit contains all the supplies that are required to load and sequence 4 chips The kit supports 4 single chip Ion Chef runs and 4 sequencer initializations 1 sequencing run sequencer initialization Library co...

Page 7: ... 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 On arrival inspect all consumables and contact Technical Support if any of the products have been damaged during shipping Kit summary Component Part No...

Page 8: ...22 on dry ice or in a closed environment containing dry ice 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 Ion 520 Chip Kit 4 pack A27761 4 chips 15 C to 30 C Ion 530 Chip Kit 4 pack A27763 4 chips Ion S5 ExT Calibration Standard For de novo sequencing applications tha...

Page 9: ...available from fisherscientific com or another major laboratory supplier Item Source Ion Chef System 4484177 Microcentrifuge 1 MLS 2 20 200 and 1 000 µL pipettes and appropriate filtered tips MLS Microcentrifuge tubes 1 5 mL or 1 7 mL MLS Vortex mixer with a rubber platform MLS Gloves powder free nitrile MLS Ice buckets and ice Nuclease free water molecular biology grade MLS Isopropyl alcohol 70 s...

Page 10: ...or is locked in the closed position during operation 2 Micropipettor A mechanical positive displacement pipettor that performs all fluid transfers during sample and chip preparation 3 Robotic arm Enables fluid transfer by the Micropipettor The arm also contains an optical sensor that reads the barcodes of instrument reagents and consumables 4 Touchscreen Provides access to all instrument functions...

Page 11: ...ed pipette tips 4 Thermal cycler sample block Performs thermal cycling of the sequencing reactions on a 96 well PCR reaction plate 5 Reagents station The position on the instrument deck of the diluted libraries NaOH and the Ion S5 ExT Chef Reagents cartridge 6 Solutions station The position on the instrument deck of the Ion S5 Chef Solutions cartridge which is maintained at room temperature 7 Reco...

Page 12: ...e Quick Start instrument setup mode User verifies the loading of a new pipette tip cartridge and an empty pipette tip rack to hold waste tips generated during the run before proceeding to Deck Scan 5 Settings button Advance to a screen providing the following options Notifications view notifications about instrument status during and between runs Instrument Settings view current settings and netwo...

Page 13: ...ies Sequencer Prepare and load a sample Create a planned run see page 18 Dilute the sample library see page 25 Prepare the consumables see page 25 Load the Ion Chef System see page 27 Start the Ion Chef run see page 37 Unload the chip for sequencing see page 42 Initialize the sequencer see page 47 Start the sequencing run see page 49 Chapter 1 Product information Workflow 1 Ion 520 Ion 530 ExT Kit...

Page 14: ...damage to the chip due to electrostatic discharge ground yourself before picking up a chip or placing a chip on a surface such as a lab bench For example touch the metal trim on the chip compartment before inserting or removing a chip from the chip clamp Protection by equipment WARNING The protection that is provided by the equipment can be impaired if the instrument is operated outside the enviro...

Page 15: ... chips prepared Remove and sequence chips within 1 hour after the Ion Chef System finishes loading them If you cannot sequence a loaded chip immediately store it within a chip storage container at 4 C until you are ready to run it up to 6 8 hours maximum IMPORTANT If you choose to store a loaded chip remove the chip from 4 C storage but keep it in the chip storage container at least 20 minutes bef...

Page 16: ...Server to view the connection status 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 Chapter 2 Before you begin Prepare the Ion Chef Instrument for use 2 16 Ion 520 Ion 530 ExT Kit Chef User Guide ...

Page 17: ...d to track samples chips and reagents throughout the workflow from template preparation on the Ion Chef Instrument through sequencing on an Ion S5 Sequencer Ion S5 XL Sequencer or Ion GeneStudio S5 Series Sequencer and subsequent data analysis Each chip that is prepared in an Ion Chef run requires its own Planned Run IMPORTANT For more information on creating a Planned Run in Torrent Suite Softwar...

Page 18: ...ake selections appropriate to your run Click Next 4 In the Kits step make the following selections a Select Ion GeneStudio S5 System from the Instrument dropdown list b Select the appropriate chip type in the Chip Type dropdown list c Select the library kit used to prepare your libraries from the Library Kit Type dropdown list d Optional For barcoded libraries select the barcode set used during li...

Page 19: ...n list in the Advanced Settings pane Select this option only if you will add Ion S5 ExT Calibration Standard to the Ion Chef Library Sample Tube Selecting this option and adding the Ion S5 ExT Calibration Standard to your library allows greater accuracy of base calling in libraries for which a reference BAM file does not exist i Click Next 5 Review the Plugins and Projects screens then make select...

Page 20: ...tion and did not select a Barcode Set in the Kits step fields appear in the Plan step where you enter the number of chips that are used enter 1 for Ion Chef ExT runs then enter the sample name and chip barcode c 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 Chapter 3 Create a Planned Run C...

Page 21: ...ck Plan Run at the bottom right of the Plan step screen to save the run 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 Chapter 3 Create a Planned Run Create a Planned Run 3 Ion 520 Ion 530 ExT Kit Chef User Guide 21 ...

Page 22: ...A libraries Leave the Barcode Set field blank RNA libraries prepared using the Ion Total RNA Seq Kit v2 Select RNA_Barcode_None from the dropdown list This will ensure that the proper trimming is performed on the resulting sequence when the RNA library does not have a barcode Flows Enter the appropriate number of flows for the read length for example 850 flows for 400 base read sequencing and 1 35...

Page 23: ... sample from the dropdown list in the Barcode column Did you select the Ion Reporter Account and the associated Ion Reporter workflow No For each sample name listed make the appropriate selections in each column in the table Yes For each sample name listed also make the appropriate selections in the Ion Reporter Workflow Relation Gender and IR Set ID columns Monitoring Thresholds Set thresholds fo...

Page 24: ...ables Start an Ion Chef run Unload the chips for sequencing Materials required Ion 520 Ion 530 ExT Kit Chef Cat No A30670 Ion 520 Chip or Ion 530 Chip Library or combined library stock solution Molecular biology grade nuclease free water P200 pipettor and filtered tips Waste container Dilute the library Sample libraries are quantified at the end of the library preparation workflow and are typicall...

Page 25: ...s of individual barcoded libraries at the same concentration for example 100 pM then dilute the combined library to a concentration recommended in the following table Dilute the sample library IMPORTANT Before proceeding dilute the library or combined library to the optimal input concentration The quality of your sequencing data relies on achieving the correct concentration of starting library Dil...

Page 26: ... diluted library or combined library see Dilute the sample library on page 25 into the Ion Chef Library Sample Tube barcoded tube from Position A of the Reagents cartridge IMPORTANT If you are performing a de novo sequencing experiment that does not include a reference BAM file add 4 μL of the Ion S5 ExT Calibration Standard to the diluted library in the Ion Chef Library Sample Tube Cap the tube v...

Page 27: ...d has been cleaned following the last use Ensure that all components are clean and dry before loading them onto the Ion Chef Instrument Ensure that the Reagents and Solutions station compartments are dry and free of condensate before loading components Follow the procedure described in the following sections to load the Ion Chef Instrument A B C D E F G H 1 2 3 4 5 6 7 8 9 10 11 12 530 DABD 0222 6...

Page 28: ...ll abort the run if tips are present in the Used position To prevent contamination change gloves immediately after moving the empty pipette tip rack to the Used Waste Pipette Tip Position Note A small amount of dried residue may be present in the tub of the empty pipette tip rack after a run This will not affect the next run 4 Unwrap a new Ion S5 ExT Tip Cartridge and remove the cover to expose th...

Page 29: ...ame Seal v2 is positioned correctly its tabs project upward and contact the heated cover A B C D E F G H 1 2 3 4 5 6 7 8 9 10 11 12 A B C D E F G H 1 2 3 4 5 6 7 8 9 10 11 12 4 1 3 2 1 Thermal cycler sample block 2 Well A1 3 Cover 4 Keyed corner Load the Reagents and Solutions cartridges IMPORTANT Thaw the Reagents cartridge at room temperature for 45 minutes before use 1 Gently tap the Ion S5 ExT...

Page 30: ...artridge A 00012216 1 D 4 C 3 B 2 1 Position A Library Sample Tube 2 Position B 2 M NaOH 3 Position C Ion S5 ExT Pellet 4 Position D Ion S5 ExT Pellet IMPORTANT Orient the Ion Chef Library Sample Tube so that the barcode is visible and oriented to the right 5 Uncap the tube of 2 M NaOH in Position B and the tubes in Positions C and D each containing an Ion S5 ExT Pellet IMPORTANT When the Reagents...

Page 31: ... sealing each centrifuge confirm that The centrifuge is load balanced with all required consumables IMPORTANT The centrifuge must be load balanced The buckets are securely seated in the centrifuge rotors The buckets are oriented correctly in the centrifuge so that they pivot outwards 2 Place a Recovery Station Disposable Lid v2 over each centrifuge by lining up the tab with the depression on the d...

Page 32: ...sposables to run the centrifuges at the rated speeds Do not remove or change the rotors To ensure normal operation inspect the buckets before each use 4 Load the Enrichment Cartridge v2 then press down on the cartridge to ensure that it is level with the instrument deck IMPORTANT Ensure that the Enrichment Cartridge v2 is loaded so that the lettering on the cartridge is right side up A B C D E F G...

Page 33: ...tached securely Note If desired you can label the tops of chips to distinguish them Do not obstruct or overwrite the chip barcode with the label 2 Load the adapter chip bucket assembly into Position 1 of the Chip loading centrifuge A B C D E F G H 1 2 3 4 5 6 7 8 9 10 11 12 1 4 2 5 3 1 Chip loading centrifuge 2 Position 1 3 Position 2 marker holes 4 Position 2 5 Position 1 marker hole Note Positio...

Page 34: ...loaded ensure that the Chip Adapter is firmly attached to its bucket and that each bucket is securely seated in the centrifuge rotors 4 Ensure the centrifuge is load balanced and the chip buckets are securely seated and oriented correctly in the centrifuge so that they pivot 90 outwards when touched Then close the lid of the Chip loading centrifuge IMPORTANT Do not obstruct or place any object on ...

Page 35: ...orrectly so that the port is oriented toward the rear of the instrument Confirm that the tube and chip buckets are seated securely in the rotor arms of the Chip loading and Recovery centrifuges and that the consumables they contain are correctly installed CAUTION To ensure correct and safe instrument operation you must confirm that all consumables are installed correctly to the deck before you sta...

Page 36: ...ly seated and level with the deck 2 Lettering on the cartridge is right side up and positioned to the right of the enrichment tubes 1 Adapter chip assembly is correctly seated in the Chip loading centrifuge bucket loaded in Position 1 with the adaptor clips inserted into the bucket slots 2 Centrifuge buckets containing the adapter chip assembly and Chip Balance loaded in Position 2 are securely se...

Page 37: ...t lead you through the instrument setup or tap Quick Start to skip the instrument setup screens and proceed to Deck Scan 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 Chapter 4 Start the Ion Chef run Start the Ion Chef run 4 Ion 520 Ion 530 ExT Kit Chef User Guide 37...

Page 38: ... scans the barcodes of all consumables and reagents to confirm their presence and compatibility During Deck Scan the touchscreen displays warnings if the Ion Chef Instrument detects missing or incompatible consumables You must address all warnings before the run can start After you address each condition tap Yes to continue IMPORTANT The Deck Scan function is not a substitute for manual inspection...

Page 39: ... a quality control QC sample that can be used to evaluate templating efficiency Depending on your selection the QC sample will be made available either during or after the run In either case you can obtain unenriched sample from the Library Sample Tube at Position A on the Reagents cartridge or enriched sample from Position E on the Enrichment Cartridge v2 By selecting You can obtain the QC sample...

Page 40: ...ls perform the following tasks a Remove the consumables from the deck then clean the instrument If possible retain the consumables for troubleshooting b Reset then attempt to start the run again If the run fails again contact Technical Support to troubleshoot the problem Record the error message for reference 11 Initialize the sequencer at least 50 minutes before the Ion Chef System finishes chip ...

Page 41: ...chment Cartridge v2 to a new labeled microcentrifuge tube d Analyze the QC sample For more information see Quality control of Ion Sphere Particles on page 67 e Close the instrument door then tap Continue to complete the run 13 When the run is complete unload the Ion Chef Instrument and sequence the chip immediately You can collect QC samples from the Reagents and or Enrichment cartridges if you ha...

Page 42: ...nload the adapter chip bucket assembly from the instrument A B C D E F G H 1 2 3 4 5 6 7 8 9 10 11 12 530 DABD0 2226 Ion Ch ef S5 Se rie s Ch ip Ba lan ce 530 DABD02226 Ion Chef S5 Series Chip Balance 1 1 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 Chapter ...

Page 43: ...Close the instrument door by first lifting it slightly to disengage the locking mechanism then push down on the door until the locks engage IMPORTANT Do not close the door by pulling it straight down from the open position You must lift the door slightly before you can close it Ensure that both sides of the door are locked after closing it 1 2 1 Lift door first 2 Lower 3 Press down to lock Chapter...

Page 44: ...dy to sequence it up to 6 8 hours maximum IMPORTANT Liquid may be present in chip wells after the Ion Chef run Do NOT remove any residual liquid from the wells 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 Chapter 4 Start the Ion Chef run Unload the chip ...

Page 45: ...n S5 Ion GeneStudio S5 Systems component positions 7 2 3 5 6 4 1 Ion GeneStudio S5 Ion GeneStudio S5 Ion GeneStudio S5 1 Touchscreen 2 Power button 3 Ion S5 ExT Sequencing Reagents cartridge 4 Chip clamp 5 Ion S5 ExT Wash Solution bottle Waste reservoir located behind the Ion S5 ExT Wash Solution bottle shown on the right 6 Ion S5 Cleaning Solution bottle 7 Waste reservoir 5 Ion 520 Ion 530 ExT Ki...

Page 46: ... its vacuum sealed bag then remove the red cap from the Ion S5 ExT Wash Solution and Ion S5 Cleaning Solution bottles immediately before installing on the instrument When a manual cleaning of the sequencer is required The Ion S5 Sequencer Ion S5 XL Sequencer and Ion GeneStudio S5 Series Sequencer require that a cleaning be performed before initialization Cleaning is normally performed automaticall...

Page 47: ... empty waste reservoir 4 Replace the expended Ion S5 ExT Sequencing Reagents cartridge with a new cartridge equilibrated to room temperature 5 Ensure the new Ion S5 ExT Wash Solution bottle is thoroughly mixed Then remove the red cap and install 1 2 3 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 Chapte...

Page 48: ...o ensure proper installation of required consumables IMPORTANT If the allowed number of post run cleans has been met the instrument prompts the user to replace the Ion S5 Cleaning Solution bottle Note If a Checking Reagent Failed warning appears see Bottle leak check fails on page 64 9 When initialization is complete 50 minutes tap Home The instrument is now ready for a sequencing run For informat...

Page 49: ... to engage the clamp then close the instrument door Start the sequencing run We recommend that you start a sequencing run as soon as possible after chip loading and instrument initialization are complete However successful sequencing runs can be started up to 24 hours after instrument initialization IMPORTANT Do not press the power button during a run Interrupting power to the instrument during a ...

Page 50: ...lose the instrument door then tap Next Note Do not remove the chip from the chip clamp until completion of the run Removing and reinserting the chip risks introducing air bubbles in the chip 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 Chapter 6 Start the...

Page 51: ...ng the instrument Touching the instrument during the sequencing run can reduce the quality of the measurements 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 Chapter 6 Start the sequencing run Star...

Page 52: ...ea with 10 bleach solution 5 Wipe the affected surfaces with 70 isopropanol then allow to air dry Reagent consumables disposal IMPORTANT Follow all applicable local state provincial and or national regulations when recycling or disposing of Ion S5 reagent consumables CO2 scrubber removal and disposal To properly dispose of the CO2 scrubber you must first remove it from the Ion S5 ExT Sequencing Re...

Page 53: ...ttles The Ion S5 ExT Wash Solution and Ion S5 Cleaning Solution bottles are made of recyclable plastic 1 Open the expended bottle by unscrewing the cap 2 Remove the cap sipper and filter then pour any residual liquid into an appropriate receptacle 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 a...

Page 54: ...e instrument IMPORTANT Although the Ion Chef Instrument cleaning routine provides some protection against contamination it is not a substitute for good laboratory technique or precautions When preparing DNA libraries for use or when preparing the Ion Chef Instrument make certain to observe sterile laboratory procedures at all times to ensure minimal contamination Materials required Gloves powder f...

Page 55: ...RTANT Do not discard the empty Ion S5 ExT Tip Cartridge Make sure to transfer the QC samples before you remove and discard the Reagents cartridge 1 Tap Open Door in the instrument touchscreen then wait for the latch to open 2 Lift the instrument door to the top of the travel until the latch mechanism engages 1 1 Hold here then lift 3 Remove then discard the PCR Plate from the thermal cycler sample...

Page 56: ... ExT Tip Cartridge from the new tip position to the waste tip position 5 Move the empty Ion S5 ExT Tip Cartridge to the waste tip position 6 Remove then discard the Ion S5 ExT Chef Reagents cartridge Ion S5 Chef Solutions cartridge Enrichment Cartridge v2 7 Remove then discard the consumables from the Recovery centrifuges including the Recovery Station Disposable Lid v2 Recovery Tubes v2 8 Remove ...

Page 57: ...en cleaning the Recovery centrifuge 2 Remove the buckets from the Recovery centrifuges Clean the inside and outside of each bucket using a lint free wipe then place the buckets on a clean dry surface while you clean the centrifuge 1 2 1 Bucket 2 Lint free wipe 3 Use lint free wipes to remove all fluid from inside the centrifuge bowl 1 2 1 Inside rim of the centrifuge 2 Bottom of the centrifuge bow...

Page 58: ...shing down on the door until the locks engage IMPORTANT Before closing the door ensure the covers of the Chip loading and Recovery centrifuges are closed 2 To start the cleaning tap Next on the Ion Chef 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 Chapter 7 Clean the Ion Ch...

Page 59: ...he Ion Chef Instrument stops ventilation then illuminates the ultraviolet UV light in the instrument for 1 minute CAUTION The Ion Chef 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 Chapter 7 Clean the Ion Chef System Clean the Ion ...

Page 60: ...hardware or software error occurred Contact Technical Support to report the problem and for further assistance The instrument stops during a run The instrument encountered an internal error 1 Record the error displayed on the instrument display then tap OK 2 Contact Technical Support to report the problem and for further assistance A consumable was improperly loaded Ensure that all consumables are...

Page 61: ...be and the empty tube 3 If the error persists after you check the consumables on the instrument deck do one of the following If you are confident that the Ion Chef Instrument is set up correctly and you are comfortable disregarding the warnings tap YES following Deck Scan to proceed with the run If the instrument cannot begin the run contact Technical Support for further assistance The instrument ...

Page 62: ... not contact the server administrator to renew the credentials 4 If the alert persists capture an image of the alert or error message if possible to help troubleshoot then contact Technical Support for further assistance Planned Run status does not advance to Planned Details The status of a successfully completed run remains listed as Reserved in Torrent Suite Software Connectivity was temporarily...

Page 63: ...e follow the onscreen prompts to restart the instrument Note In some cases the instrument restarts automatically after software installation If a message states No Connectivity to Torrent Server No Connectivity to ftp server or Network Manager not connected disconnect and re connect the ethernet cable confirm that the router is operational and verify that the network is up and running For any othe...

Page 64: ... was not tight Bottle was damaged or defective 1 Finger tighten the bottles 2 If the bottle continues to leak replace the bottle 3 If leak check continues to fail contact Technical Support Appendix A Troubleshooting Ion S5 Ion GeneStudio S5 Systems setup and operation A 64 Ion 520 Ion 530 ExT Kit Chef User Guide ...

Page 65: ...Settings4Clean Instrument The instrument door unlocks allowing access to the consumables 2 Remove the Ion S5 ExT Wash Solution bottle to access the waste reservoir then remove and empty the waste reservoir 1 2 3 3 Reinstall the empty waste reservoir and a used Ion S5 ExT Wash Solution bottle 4 Ensure that the Ion S5 ExT Sequencing Reagents cartridge and Ion S5 ExT Wash Solution bottle are properly...

Page 66: ... Note If a power failure or abort occurs during the second of two runs started after a single initialization a manual cleaning is sufficient see Perform a manual cleaning of the sequencer on page 65 If the number of flows that occurred before a power failure or abort is unknown perform an instrument reset run To perform an instrument reset run use the following procedure before reinitialization 1 ...

Page 67: ...ample from the tube on the Enrichment Cartridge v2 at position E For details see the Ion Sphere Particles Quality Assessment for the Ion Proton and Ion S5 Systems Using the Guava easyCyte 5 Benchtop Flow Cytometer User Bulletin Pub No MAN0007496 available at thermofisher com Maintain the Ion Chef System For further information on the following Ion Chef System maintenance procedures see the Ion Che...

Page 68: ...entation provided by the manufacturer of the instrument or device Before handling chemicals read and understand all applicable Safety Data Sheets SDSs and use appropriate personal protective equipment gloves gowns eye protection and so on To obtain SDSs see the Documentation and Support section in this document Symbols on this instrument Symbols may be found on the instrument to warn against poten...

Page 69: ...ts usuels non soumis au tri sélectif MISE EN GARDE Pour minimi ser les conséquences négatives sur l environnement à la suite de l éli mination de déchets électroniques ne pas éliminer ce déchet électro nique avec les déchets usuels non soumis au tri sélectif Se conformer aux ordonnances locales sur les dé chets municipaux pour les disposi tions d élimination et communiquer avec le service à la cli...

Page 70: ...t safety General CAUTION Do not remove instrument protective covers If you remove the protective instrument panels or disable interlock devices you may be exposed to serious hazards including but not limited to severe electrical shock laser exposure crushing or chemical exposure Physical injury CAUTION Moving Parts Moving parts can crush pinch and cut Keep hands clear of moving parts while operati...

Page 71: ...a result of a reaction with parts of the equipment or with material contained in the equipment The instrument is properly decontaminated a if hazardous material is spilled onto or into the equipment and or b prior to having the instrument serviced at your facility or sending the instrument for repair maintenance trade in disposal or termination of a loan decontamination forms may be requested from...

Page 72: ...automatic laboratory equipment for analysis and other purposes EMC Reference Description Directive 2014 30 EU European Union EMC Directive FCC Part 15 U S Standard Industrial Scientific and Medical Equipment AS NZS 2064 Limits and Methods of Measurement of Electromagnetic Disturbance Characteristics of Industrial Scientific and Medical ISM Radiofrequency Equipment ICES 001 Issue 3 Industrial Scien...

Page 73: ...e safety glasses gloves or protective clothing Minimize the inhalation of chemicals Do not leave chemical containers open Use only with adequate ventilation for example fume hood Check regularly for chemical leaks or spills If a leak or spill occurs follow the manufacturer s cleanup procedures as recommended in the SDS Handle chemical wastes in a fume hood Ensure use of primary and secondary waste...

Page 74: ...nstitution requirements before working with potentially biohazardous materials Follow all applicable local state provincial and or national regulations The following references provide general guidelines when handling biological samples in laboratory environment U S Department of Health and Human Services Biosafety in Microbiological and Biomedical Laboratories BMBL 5th Edition HHS Publication No ...

Page 75: ...010810 Ion GeneStudio S5 Instrument User Guide MAN0017528 Ion S5 and Ion S5 XL Instrument User Guide MAN0010811 Ion S5 Controls Kit Plus Product Information Sheet MAN0016206 Torrent Suite Software 5 12 User Guide MAN0017972 Torrent Suite Software 5 12 Help MAN0017973 Ion Sphere Particles Quality Assessment for the Ion Proton and Ion S5 Systems Using the Guava easyCyte 5 Benchtop Flow Cytometer Use...

Page 76: ...afety Data Sheets SDSs also known as MSDSs Note For SDSs for reagents and chemicals from other manufacturers contact the manufacturer Limited product warranty 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 questi...

Page 77: ......

Page 78: ...0 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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