Instrument maintenance and shutdown procedures for extended site closures

This bulletin provides detailed instructions for shutting down and maintaining Illumina instruments in the event of lab closure. Lab closure reasons may include but are not limited to public health events, natural disasters, or government closures.

Read Illumina Statement on Novel Coronavirus and follow the Illumina Perspective on the Novel Coronavirus SARS-CoV-2 (2019-nCoV) Outbreak web page for further updates.

General instructions for shutting instruments down for an extended period of time

General instructions for sequencing systems [excluding the NovaSeq X/X Plus]

1. Perform a maintenance/manual/Standby wash (Standby wash for MiSeq only) using Tween 20 and NaOCl (if applicable), instructions are found in the instrument system guides.

2. Perform another maintenance/manual/Standby wash (Standby wash for MiSeq only) using laboratory-grade water to remove Tween from the system.

3. If possible, perform the above steps every 30 days.

General instructions for all systems

1. Shut down procedures:

• If employees will be in the lab, leave instrument powered on while idle.

• If lab is completely shutting down (no employees on site or possibility of power being shut off), power off the instrument via normal processes in the instrument system guide.

1. Keep the instrument off until normal work schedules permit.

Upon permanent return to work

1. Power on the instrument.

2. Perform two maintenance/manual washes to rehydrate the fluidics system.

• Note: If additional maintenance/manual/Standby wash using laboratory-grade water was not performed prior to instrument shutdown, perform three maintenance/manual washes to rehydrate the fluidics system and run system checks to test the fluidics delivery.

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Instrument-specific instructions for Maintenance Best Practices during normal operation

MiSeq

In the event of an extended laboratory shutdown, the MiSeq instrument can be placed into Standby mode by performing a Standby wash. When in Standby mode, perform additional Standby washes every 30 days that the instrument is idle. To switch the instrument out of Standby mode, perform a power cycle (follow the shutdown instructions below and wait at least 1 minute before toggling the power switch back on) and then a Maintenance wash. If the instrument has been idle for a significant period, additional Maintenance washes can be performed to ensure that the fluidics system is ready for a sequencing run.

Instructions for performing Standby and Maintenance washes are found in the MiSeq System Guide.

Shutdown the Instrument:

1. Close MiSeq Control Software.

2. Make sure that no other programs are running, then shut down your PC from the Windows Start button.

3. After the PC has shut down, toggle the power switch at the back of the MiSeq to turn off the instrument.

NextSeq 500/550

For the NextSeq 500/550, perform a Quick wash every 14 days that the instrument is idle, leaving the reagent wash cartridge and buffer cartridge in place.

Instructions for performing the Quick Wash are found on Page 36 of the NextSeq 500/550 Sequencing System Guide.

Shutdown the Instrument:

1. Select Manage Instrument. Note: To shutdown the NextSeq 550Dx instrument in research mode, see NextSeq 550Dx Reboot and Shut Down Options on page 67 of the NextSeq 500/550 Sequencing System Guide.
2. Select Shutdown Options.

3. Select Shutdown.

4. The Shutdown command safely shuts down the software and turns off instrument power. CAUTION: Do not relocate the instrument. Moving the instrument improperly can affect the optical alignment and compromise data integrity. If instrument relocation is necessary, contact your Illumina representative.

MiniSeq

For the MiniSeq instruments, perform a Quick wash every 7 days that the instrument is idle, leaving the reagent wash cartridge and buffer cartridge in place.

Instructions for performing the Quick Wash are found on Page 26 of the MiniSeq System Guide.

Shutdown the Instrument:

1. Select Manage Instrument.

2. Select Shutdown Options.

3. Select Shutdown.

4. The Shutdown command safely shuts down the software and turns off instrument power. CAUTION: Do not relocate the instrument. Moving the instrument improperly can affect the optical alignment and compromise data integrity. If instrument relocation is necessary, contact your Illumina representative.

iSeq100

Because the fluidics system on the iSeq 100 is housed within the reagent cartridge, no additional steps are required for idling the iSeq 100. For extended closures, shut down the instrument by navigating to the hamburger menu in the top left corner of the Control Software and selecting Shutdown System. After the instrument has been shut down, toggle the power switch on the back of the instrument to fully power down the system.

More information on the iSeq 100 is found in the iSeq 100 System Documentation.

HiSeq 2500/3000/4000/X

To idle the HiSeq instrument for 10 days or less, use the following instructions:

1. Perform a maintenance wash to flush the system.

2. Leave the flow cell on the flow cell stage with the flow cell lever in position 2. Leave the manifolds in the raised position.

3. Load 10 ml laboratory-grade water in each position in the reagent racks, then lower the sippers.

4. Load 1 ml laboratory-grade water in the loading station position (HiSeq 2500 only).

5. Before using the instrument, perform a water wash with laboratory-grade water.

If the instrument will be idle for more than 10 days, shut down the instrument using the following instructions:

1. Perform a maintenance wash to flush the system.

2. Remove the flow cell from the flow cell stage.

3. Wipe the surface of the flow cell holder using an alcohol wipe or a lint-free tissue moistened with ethanol or isopropanol. CAUTION: Do not allow alcohol to drip into the vacuum holes or around the manifolds. Use a low-lint lab tissue to dry the stage, if necessary.

4. Load 10 ml laboratory-grade water in each position in the reagent racks, then lower the sippers.

• (HiSeq 2500 only) Load 1 ml laboratory-grade water in each loading station position.

1. Turn off the instrument.

More information on HiSeq systems is found in the respective HiSeq System Guides found here:

• HiSeq 2500 | HiSeq 3000 | HiSeq 4000 | HiSeq X

NextSeq 1000/2000

Because the fluidics system on the NextSeq 2000 is housed within the reagent cartridge, no additional steps are required for idling the NextSeq 2000.

Shutdown the Instrument:

• Eject used reagent cartridge from instrument prior to shutting down NextSeq 1000/2000.

• From the menu, select Shut Down Instrument.

• If the system does not shut down, hold the power button on the right side of the instrument until the lights fade.

• When the power button pulses, press the power off (Ο) side of the toggle switch on the rear panel. The power button might continue to pulse after the power is turned off.

More information on the NextSeq 1000/2000 can be found in the NextSeq 1000/2000 Product Documentation .

NovaSeq 6000

The NovaSeq 6000 instrument requires a maintenance wash every 14 days that instrument has been idle or if a four-lane run with an automatic post-run wash has not been completed within the previous 14 days.

Instructions for performing the Maintenance wash on the NovaSeq 6000 instrument are found on Page 61 of the NovaSeq 6000 System Guide.

If employees will be in the lab, leave NovaSeq 6000 powered on while idle. If lab is completely shutting down, power off the NovaSeq 6000.

Shutdown the instrument:

1. Choose Instrument Shutdown from NovaSeq Control Software hamburger menu.

2. When monitor shuts down, use the toggle switch at rear right to switch off the instrument.

NovaSeq X/X Plus

If the NovaSeq X/X Plus will be idle for more than 2 days, the instrument should be left as-is after the most recent sequencing Post-Run Wash completes (with a used reagent cartridge and used flow cell present). This will prevent the fluidics system from drying out.

In the event of an extended instrument shutdown (>14 days), follow the instructions below:

1. Leave the used sequencing consumables from the most recent sequencing run in place after the Post Run Wash completes.

   1. Do not remove the used flow cell or sequencing reagent cartridge.

   2. Remove and dispose of the the spent reagents in the large and small waste bottles as detailed in the NovaSeq X Plus Product Documentation
2. Power off the NovaSeq X /X Plus instrument

   1. From the NovaSeq X Series Control Software Home screen, select the instrument icon to open the global navigation menu, and select Settings.

   2. From the Settings menu, select Shutdown

   3. Wait 2 minutes for the instrument computer to power down and the monitor is dark.

   4. Toggle the power switch to the off position on the back right side of the instrument.

3. Perform a maintenance wash before using the instrument for sequencing again as detailed in the NovaSeq X Plus Product Documentation

iScan

Shutdown the iScan System:

1. Remove BeadChips.

   1. Open the iScan Reader tray.

   2. To remove the carrier, lift it straight up and out of the tray.

2. Close the iScan Control Software.

   1. Select the menu button in the upper left corner of the screen.

   2. Select Exit.

3. From the Windows Start menu on the iScan System computer, select Shutdown.

4. Toggle the Power switch on the back panel of the iScan Reader.

For more information on maintenance or shutting down the iScan instrument, refer to the iScan System Guide.

Tecan

Preparing the Tecan for extended idle period:

1. Follow Cleaning the Tecan instructions from the Infinium Assay Lab Setup and Procedures Guide.
2. After washing with 10% bleach.

   1. Fully remove the bleach solution from the carboy and refill with lab-grade water.

   2. Perform two additional washes on the Tecan with lab-grade water.

3. Repeat above steps every 30 days if possible, otherwise leave the system powered off.

4. Powering off the Tecan.

• If lab personnel will be available, leave the Tecan powered on.

• If no lab/institution personnel will be available, power off the Tecan.

Powering off the Tecan:

1. Dry out the Tecan fluidics system.

   1. Empty out the water tank.

   2. Run two system washes to dry out the lines.

2. Power down the water circulator/Te-Flow.

   1. Power down the water circulator.

   2. Drain the water tubing to and from the Te-Flow.

   3. Rinse the Te-Flow pan with water and let drain to waste.

   4. Empty waste container.

3. Shut down the Illumina Automation Control (IAC) software.

4. Shut down the computer.

5. Power down the Tecan.

Upon permanently returning to work:

1. Power on the Tecan.

2. Refer to the following sections in the Infinium Assay Lab Setup and Procedures Guide under Robot Usage and Maintenance.

• Preparing the Robot for Use (perform at least two bleach washes).

• Testing Volume Accuracy of the Tecan Tips.

For more information on maintaining or shutting down the Tecan instrument, refer to the Infinium Assay Lab Setup and Procedures Guide.

For any feedback or questions regarding this article (Illumina Knowledge Article #2336), contact Illumina Technical Support [e-mail].