Thermo Scientific Ion GeneStudio S5 Prime User Manual

For Research Use Only. Not for use in diagnostic procedures.
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

Thermo Scientific Ion GeneStudio S5 Prime Specifications

General

Output per Run	Up to 50 Gb
Sample Type	DNA, RNA
Connectivity	Ethernet, USB
Maximum Reads per Run	Up to 80 million
Operating Temperature	15°C to 30°C
Operating Humidity	20% to 80% non-condensing
Platform Type	Next-Generation Sequencing
Technology	Semiconductor Sequencing
Applications	Exome Sequencing, Targeted Sequencing, Transcriptome Sequencing
Chip Types	Ion 530
Voltage Requirements	100-240 V AC
Workflow	Automated

Summary

Ion 520™ & Ion 530™ ExT Kit – Chef USER GUIDE

Chapter 1 Product information

Product description

Details the contents and purpose of the Ion 520™ & Ion 530™ ExT Kit – Chef for sequencing workflow.

Kit contents and storage

Details the components included in the kit and recommended storage conditions for optimal performance.

Kit summary

Kit components

Required materials not supplied

About the Ion Chef™ System

Provides an overview of the Ion Chef™ System's capabilities, automation, and integration with Torrent Suite™ Software.

Ion Chef™ Instrument components

Identifies and describes the major external and internal components of the Ion Chef™ Instrument.

Interior hardware and consumables

Illustrates and details the internal stations and consumables used in the Ion Chef™ Instrument for chip preparation.

About the Ion Chef™ System touchscreen interface

Explains the features and functions of the Ion Chef™ System's touchscreen interface for operation and maintenance.

Workflow

Chapter 2 Before you begin

Precautions

Covers essential safety guidelines, including avoiding contamination and chip damage, and equipment protection.

Guidelines for using Ion Chef™ consumables and reagents

Provides best practices for handling and using Ion Chef™ consumables and reagents to ensure proper function.

Prepare the Ion Chef™ Instrument for use

Details the necessary steps to prepare the Ion Chef™ Instrument before loading consumables and starting a run.

Chapter 3 Create a Planned Run

Create a Planned Run

Provides step-by-step instructions for creating a Planned Run using the Torrent Suite™ Software.

Planned Run workflow key fields

Chapter 4 Start the Ion Chef™ run

Materials required

Dilute the library

Explains how to dilute libraries to the optimal concentration for use in Ion Chef™ template runs.

Guidelines for library dilution

Dilute the sample library

Details the procedure for diluting individual or combined sample libraries to the correct input concentration.

Dilute the control library

Prepare the consumables

Details the steps for preparing the necessary cartridges and consumables before loading them into the instrument.

Add the diluted libraries to the Ion Chef™ Library Sample Tube

Instructs on pipetting the diluted library into the correct tube for the Ion Chef™ Library Sample Tube.

Load the Ion Chef™ System

Guides the user through loading all required cartridges, tubes, and plates into the Ion Chef™ Instrument.

Load the tip racks and PCR Plate

Details the process of loading new tip cartridges and the PCR plate into the instrument.

Load the Reagents and Solutions cartridges

Instructs on how to load the Reagents and Solutions cartridges into the correct stations on the Ion Chef™ Instrument.

Load the Recovery Tubes and Enrichment Cartridge v2

Guides the user in loading Recovery Tubes and the Enrichment Cartridge v2 into the respective centrifuge and station.

Load the Chip-loading centrifuge

Provides detailed steps for assembling and loading the chip into the chip-loading centrifuge.

Confirm that consumables are correctly installed

Ion Chef™ pre-run checklist

Start the Ion Chef™ run

Guides the user through initiating the Ion Chef™ run via the instrument touchscreen interface.

Unload the chip for sequencing

Details the procedure for safely removing the chip from the Ion Chef™ Instrument after the run is complete.

Chapter 5 Initialize the sequencer

Ion S5™/Ion GeneStudio™ S5 Systems component positions

Before you begin

Initialize the sequencer

Details the step-by-step procedure for initializing the sequencer, including cartridge and waste handling.

Chapter 6 Start the sequencing run

Chip handling guidelines

Start the sequencing run

Guides the user through initiating the sequencing run after chip loading and initialization are complete.

Clean or decontaminate the sequencer

Chapter 7 Clean the Ion Chef™ System

About the cleaning protocol

Clean the Ion Chef™ Instrument

Provides instructions for cleaning the Ion Chef™ Instrument after each run to prevent contamination.

Remove and dispose of used consumables

Inspect and clean the Recovery centrifuges and buckets

Start the cleaning

Provides instructions on how to initiate the automated cleaning cycle for the Ion Chef™ Instrument.

APPENDIX A Troubleshooting

Ion Chef™ System setup and operation

Planned Run status does not advance to "Planned"

Ion S5™/Ion GeneStudio™ S5 Systems setup and operation

Instrument alarms and events

Initialization—General errors

APPENDIX C Safety

Instrument safety

Electrical safety

Cleaning and decontamination

Ultraviolet (UV) Safety

Instrument safety – Ion S5™/Ion GeneStudio™ S5 Systems

Chemical safety

Biological hazard safety