The ElysION™ is a fully automated sample-to-answer sequencing solution with three integrated MinION™ Mk1D devices and onboard computing. It is designed to bring streamlined genomics into the lab by offering a range of end-to-end sequencing workflows for a broad field of research applications.

The ElysION is a combined liquid handling and sequencing device that is intended for use in a laboratory setting for the preparation and sequencing of nanopore libraries from a range of input materials.

This device is for research use only.

Current supported Oxford Nanopore workflows:

• Rapid barcode sequencing
• Native barcode sequencing
• Nanopore-only Microbial Isolate Sequencing Solution (NO-MISS)
• Microbial amplicon barcode sequencing for 16S and ITS
• Rapid PCR barcode sequencing
• Metagenomics

Current supported Oxford Nanopore kits:

• Rapid Barcoding Kit 96 V14 (SQK-RBK114.96)
• Native Barcoding Kit 96 V14 (SQK-NBD114.96)
• Rapid PCR Barcoding Kit 24 V14 (SQK-RPB114.24)
• Microbial Amplicon Barcoding Kit 24 V14 (SQK-MAB114.24)
• Flow Cell Wash Kit (EXP-WSH004)
• Flow Cell Wash Kit XL (EXP-WSH004-XL)

Current supported flow cells:

• MinION/GridION Flow Cells R10.4.1 (FLO-MIN114)

Package includes:

• 1x ElysION Sample Preparation Device
• 1x ElysION Integration Kit - MinION
• 1x ElysION Control Unit - MinION
• 3x MinION Mk1D sequencing devices
• 3x MinION/GridION Flow Cells R10.4.1 (FLO-MIN114)
• 1x Rapid Barcoding Kit 96 V14 (SQK-RBK114.96)
• 1x Software Licence and Device Warranty (12 months)

Also included:

• Installation of instrument and software
• Installation qualification
• On-site training

Attach the cables and peripherals to the ports shown in the diagram. The USB-C port can be used to connect an adapter to plug in USB Type A cables.

Attach the cables and peripherals to the ports shown in the image.

During the preparation of the device and ahead of starting a run, there are four sequencing run variables that can be set for the Run plan.

This variable gives you the option to set the maximum length of time (in hours) the instrument will sequence for or the option to run until the flow cell pores are depleted (5% of total pore count). When either the time limit has been reached or the pores have been depleted, the instrument will stop sequencing and proceed to the next step in the workflow.

This variable allows you to set a maximum sequencing data output (in Gbases). Once this data target has been achieved, the instrument will stop sequencing and proceed to the next step in the workflow. Alternatively, where no data target is set, sequencing will stop according to the set 'Sequencing time limit' variable.

Note: Sequencing will stop when either the set sequencing time limit or set data target has been met. For example, if the sequencing time limit is set to 72 hours and the data target is set to 20 Gbases, and sequencing produces 20 Gbases in 48 hours, sequencing will stop before the 72 hours time limit.

This variable allows you to decide what happens to the flow cell once sequencing has completed. Flushing prepares the flow cell for return to Oxford Nanopore for recycling. Washing cleans the flow cell to allow multiple use of the same flow cell.

Note: Flush/Wash choices will require different reagents to be used. Washing will require an additional Oxford Nanopore Flow Cell Wash Kit (EXP-WSH004) or Flow Cell Wash Kit XL (EXP-WSH004-XL).

This variable is an optional toggle feature in the UI which allows you to turn on or off the write out to a POD5 file format.

All ElysION workflows require a sample sheet in order to perform a workflow. The sample sheet performs several functions:

• Instructs the instrument on how many samples to process.
• Instructs the instrument if normalisation is required and the volumes of sample to take forward.
• Instructs the instrument on which barcodes to attach to samples and to include in sequencing and analysis.

Sample sheets contain unique parameter values required for the specific workflow being run. You can alter the parameters to ensure correct preparation of samples. If sample sheet parameters do not match the workflow assay or are in the incorrect format, the sample sheet will be rejected.

To avoid issues when writing a new sample sheet, we recommend that you always design a new sample sheet from the template provided by Oxford Nanopore.

Values which must not be altered on the sample sheet (highlighted in pink):

Values which can be altered on the sample sheet (highlighted in green):

Rules of editing values on the sample sheet:

• library_id: Any text to identify one library from another in a human readable format.
• created_by: Any text to identify the user who wrote the sample sheet in a human readable format.
• created_at: The time stamp that the sample sheet file was created. This must be in the ISO 8601 format.

ISO 8601 formatting:

• 2024-06-21: The date (Year-Month-Day).
• T: The separator between the date and time (standard in ISO 8601).
• 14:07:14: The time in 24-hour format (Hours:Minutes:Seconds).
• +01:00: The time zone offset from UTC (in this case, it is 1 hour ahead of UTC).

sample_count: The exact number of samples being processed by the instrument given as an integer value. This value must be within the range possible for the workflow being prepared (see workflow specific documentation).

well_id: The id of the wells that the samples start in. This must always start at A1 and continue in a column wise list, with no gaps. The total number of well ids listed in the sample sheet must be equal to the sample count value also provided.
Examples of correct and incorrect well_id configurations are shown in the Table below:

Correct well_id configuration	Incorrect well_id configuration
A1, B1, C1, D1, E1, F1, G1, H1, A2 and sample count = 9	B1, C1, D1, E1, F1, G1, H1, A2, B2 (A1 missing)
	A1, B1, C1, D1, F1, G1, H1, A2, B2 (E1 missing)
	A1, A2, A3, A4, A5, A6, A7, A8 (Row format)
	A1, B1, C1, D1, E1, F1, G1, H1 and sample count = 9 (only 8 samples listed)

barcode: This list of barcode ids specifies which barcode from Oxford Nanopore barcode plate is delivered to each sample (as specified in the well_id column). The first barcode can be taken from any position in the barcode plate however, all subsequent barcodes must follow in a sequential order. The total number of barcode ids must match the total number of samples provided. Each barcode can only be used once and must be formatted as a two-digit number.
Examples of correct and incorrect barcode configurations are shown in the Table below:

Correct barcode configuration	Incorrect barcode configuration
barcode01, barcode02, barcode03, barcode04, barcode05, barcode06 and sample count = 6	barcode03, barcode04, barcode05, barcode06, barcode01, barcode02 (not sequential)
barcode06, barcode07, barcode08, barcode09, barcode10, barcode11, and sample count = 6	barcode01, barcode02, barcode03, barcode04, barcode05, barcode08 (not sequential)
	barcode08, barcode09, barcode010, barcode11, barcode12, barcode13 (barcode010 has 3 digits)
	barcode01, barcode02, barcode03, barcode04, barcode05, barcode06 and sample count = 8 (only 6 samples listed)

sample_type: The sample type flag which is used during post-basecalling analysis. Defaults as 'sample' if post-basecalling analysis is not required. If you plan to do analysis, see the workflow specific documentation for further instructions.

barcode_set: The barcode set identifies the specific set of barcodes to be used for the library preparation where there are 3 sets of 24 barcodes in a 96 well plate for the sequencing kit (i.e. Rapid PCR Barcoding Kit 24 V14 (SQK-RPB114.24) and Microbial Amplicon Barcoding Kit 24 V14 (SQK-MAB114.24)). To select the first set of barcodes from the 96 well plate (columns 01 to 03) for your library preparation, enter set01 under the barcode_set column for your sample. For the second set of barcodes (columns 05 to 07), enter set02, or for the third set of barcodes (columns 09 to 11), enter set03.

See example sample sheet below:

The first barcode can be taken from any of the 3 barcode sets in the 96 well plate however, all subsequent barcodes must follow in a sequential order as shown in the Table below:

well_id	barcode	barcode_set
A1	barcode24	set01
B1	barcode01	set02
C1	barcode02	set02

sample_id: The sample id is user-defined and can be used to track a sample from input to results.

To include automated sample normalisation, an additional column named sample_volume must be added to the sample sheet as follows.

sample_volume: The sample volume flag indicates that automated sample normalisation is to be implemented and should be added to the right of the sample_id flag. Rows underneath must contain the volume of sample to be transferred to each well of the PCR plate (in µl). This volume will be automatically normalised to the required input volume using nuclease-free water (NFW).
If the sample_volume column is absent, no automated sample normalisation will be implemented.

Sample volumes will be specific to each workflow therefore, we recommend that you check the specific protocol for this information.

In the example below, 5 µl of sample will be transferred from the sample plate to the PCR plate and normalised to the required sample volume taken forward with NFW (e.g. 30 µl for RBK using gDNA or 27 µl for RBK using amplicons).

There is an option to perform QC checks and manual sample normalisation during the automated library preparation.

In order to do this, the Pause for QC variable has to be turned on when configuring a custom method (see section 16 below). Enabling this feature will instruct the ElysION to automatically pause for QC checks and manual sample normalisation to be performed.

Refer to the specific protocols for more information about this variable and how to normalise your samples.

If you wish to alter the default variables for your assay, follow the instructions below.

The Table below describes the list of labware compatible with the ElysION device.

Labware	Recommended supplier	Product code
Hard-Shell® 96-Well PCR Plates, low profile, thin wall, skirted	Bio-Rad™	HSP9611
Nunc™ 96 Well Polypropylene 2 ml DeepWell Plate	Thermo Scientific	95040452
1000 µL Disposable Tips - Filtered, Pure, Single Stack	Tecan	30057817
200 µL Disposable Tips - Filtered, Pure, Single Stack	Tecan	30057815
50 µL Disposable Tips - Filtered, Pure, Single Stack	Tecan	30057813
10 µL Disposable Tips - Filtered, Pure, Single Stack	Tecan	30104974
LiHa empty Disposable Tip Box Small	Tecan	30058506
LiHa empty Disposable Tip Box Large	Tecan	30058507
Waste bin	Tecan	30185747
Reservoir Plate	Porvair	390015
Azenta PCR Plate Lid	Azenta	4ti-0291
Screw cap micro tube 2 ml, sterile	Sarstedt	72.694.006
Screw cap micro tube 0.5 ml, sterile	Sarstedt	72.785.005

Changing the system password

Note: The instructions below will apply for your username.

1. Open command line on the Linux compute.

2. Type: sudo passwd username

• This will prompt you to enter your current password on the first attempt.

3. Enter a new UNIX password: Type new password and press enter.

4. Re-enter the new UNIX password: Type new password again and press enter.

5. passwd: Password successfully changed

Changing the system username

• We do not recommend the changing of usernames.

For full details on the maintenance and decontamination procedures, refer to the ElysION Operating manual provided with your device.

The device should be cleaned with any of the listed agents and dried with a lint-free cloth. Use of any other chemical agents than those listed below or listed in the full ElysION Operating manual may cause damage to the instrument or risk injury to you.

Cleaning agent	Specification
DI water	Distilled or deionized water
Alcohol	70% ethanol or 100% isopropanol (2‑propanol)
Weak detergent	Liqui-Nox
Disinfectant	Bacillol plus, Bomix, Lysetol FF
System liquid	Distilled or deionized water
Base	0.025 to 0.25 mol/l sodium hydroxide
Bleach	6% sodium hypochlorite
RNase AwayTM decontamination reagent	Alkali hydroxide <0.1%

Refer to the ElysION Operating manual included with your ElysION device for details of the maintenance schedule.

• Empty both waste containers.
• Either decontaminate or replace with new waste containers.

Clean the following with 70% ethanol:

• Waste drawer
• DiTi drop station
• ElysION robot touch screen monitor

Refer to the ElysION Operating manual for more information.

1. On the touch screen monitor, click the Export Logs application from the desktop.

2. Copy the generated logging snapshot to a USB drive.

1. Open Show Applications in the bottom left corner.

2. Select the Elysion Logs application.

3. Enter the compute password.

4. Copy the generated logging snapshot to a USB drive.

ElysION liquid handler

• The serial number for the ElysION liquid handler is found on the rear panel of the device, as highlighted in the image below:

Compute control unit

• The serial number for the compute control unit can be found on the rear side of the unit, as shown in the image below:

Report issues to Nanopore Support with the serial numbers for both the liquid handler and compute unit and the logging snapshots from both the Windows and Linux computes attached.

• If the device does not switch on, contact your customer support representative and include the device serial numbers in the description of your issue.

• Contact your customer support representative.

• Oxford Nanopore can provide support to connect your instrument to an internal network to allow automated data offload from the ElysION device to your long-term storage.

• Contact your customer support representative and include the device serial numbers in the description of your issue and attach copies of your logging data.

• Contact your customer support representative and include the device serial numbers in the description of your issue and attach copies of your logging data.

• Contact your customer support representative and include the device serial numbers in the description of your issue and attach copies of your logging data.