Cytek Biosciences Aurora User manual

Aurora™ User’s Guide

Copyrights
©2017, Cytek Biosciences Inc. All rights reserved. No part of this publication may be reproduced, transmitted, tran-
scribed, stored in retrieval systems, or translated into any language or computer language, in any form or by any means:
electronic, mechanical, magnetic, optical, chemical, manual, or otherwise, without prior written permission from Cytek
Biosciences.
The information in this guide is subject to change without notice. Cytek Biosciences reserves the right to change its prod-
ucts and services at any time to incorporate the latest technological developments. Although this guide has been pre-
pared with every precaution to ensure accuracy, Cytek Biosciences assumes no liability for any errors or omissions, nor
for any damages resulting from the application or use of this information. Cytek Biosciences welcomes customer input
on corrections and suggestions for improvement.
Trademarks
Cytek, the Cytek logo, and all other trademarks are property of Cytek Biosciences. © 2017 Cytek
FCC Information
WARNING: Changes or modifications to this unit not expressly approved by the party responsible for compliance could
void the user's authority to operate the equipment.
NOTICE: This equipment has been tested and found to comply with the limits for a Class A digital device, pursuant to Part
15 of the FCC Rules. These limits are designed to provide reasonable protection against harmful interference when the
equipment is operated in a commercial environment. This equipment generates, uses, and can radiate radio frequency
energy and, if not installed and used in accordance with the instruction manual, can cause harmful interference to radio
communications. Operation of this equipment in a residential area is likely to cause harmful interference in which case
the user will be required to correct the interference at his or her own expense.
Shielded cables must be used with this unit to ensure compliance with the Class A FCC limits.
This Class A digital apparatus meets all requirements of the Canadian Interference-Causing Equipment Regulations.
Cet appareil numérique de la classe A respecte toutes les exigences du Réglement sur le matériel brouilleur du Canada.
CDRH Information
This equipment complies with CDRH Class I requirements.
Regulatory Information
For Research Use Only. Not for use in diagnostic or therapeutic procedures.
History
Revision Date Change
52-70001-0A 10/2017 Initial release

iii
Chapter 1: Introduction 7
About this Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Safety Symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
General Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Electrical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Biological Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Chapter 2: Overview 9
Cytometer Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Fluidics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Software Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Spectral Unmixing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Understanding Full Spectrum Flow Cytometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Reference Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Chapter 3: Startup & Shutdown 17
Filling the Sheath and Emptying the Waste . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Filling the Sheath . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Emptying the Waste . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Starting Up the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Shutting Down the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Chapter 4: QC & Setup 21
Daily QC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Performing Daily QC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
QC Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Instrument Setup - Reference Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Creating Reference Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Running Reference Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Updating Reference Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Levey-Jennings Tracking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Gain Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Alarm Ranges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Chapter 5: Acquisition 31
Raw vs Unmixed data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Unmixing and Compensation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Contents

iv Aurora User’s Guide
Setting Up an Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Experiment Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Creating a New Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Unmixing Workflows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Live Unmixing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Post-Acquisition Unmixing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Chapter 6: Advanced Unmixing 47
Unmixing in the Analysis Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Virtual Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Chapter 7: Library, Preferences, and Users 55
Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Fluorescent Tags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
User Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Worksheet Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Experiment Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Worksheet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Gates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Fonts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Notifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
QC Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Managing Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Use Time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Chapter 8: Maintenance 71
Maintenance Schedule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Scheduled Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Unscheduled Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Cleaning the SIT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Purging the Sheath Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Removing Air Bubbles from the Flow Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Cleaning the Flow Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Decontaminating the Fluidics System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Cleaning the External Surfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Inspecting the Fluidics Lines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Replacing the Sheath Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Replacing the SIT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

v
Chapter 9: Troubleshooting 81
Chapter 10: Glossary 83
Chapter 11: Specifications 87
Cytometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Fluidics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Fluorescence Sensitivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Workstation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Installation Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Chapter 12: Supplies and Replacement Parts 91

vi Aurora User’s Guide

Chapter 1: Introduction 7
1
Introduction
About this Guide
This manual provides information on the Aurora flow cytometer, daily workflow, SpectroFlo™
software features, cytometer specifications, and instrument maintenance. It also includes
troubleshooting tips and service information.
Safety
Safety Symbols
The Aurora is intended for research use only. Not for diagnostic or therapeutic procedures.
The following table lists symbols used throughout this guide.
General Safety
• Do not place any object on top of the instrument.
• Before turning on the cytometer, visually inspect all containers. Wear the recommended
protective laboratory attire such as protective gloves, eyewear, and lab coat.
• Purge the sheath filter if air bubbles are visible in the sheath filter, or if the plenum or sheath
container have run dry.
• Fill the sheath container as needed. Never use tap water as sheath solution.
• Do not run bleach or detergent through the sheath filter. It is difficult to remove cleaning
solutions from the sheath filter.
Symbol Meaning
Caution: hazard or unsafe practice that could result in material damage,
data loss, minor or severe injury, or death
Risk of electric shock
Biological risk

8Aurora User’s Guide
• Check the cytometer periodically for fluid leaks or crimped lines. If evidence of a leak is
detected, contact Cytek Technical Support immediately. Do not attempt to repair the
instrument.
• When performing daily QC, always select the correct bead lot number.
Electrical Safety
• Do not place liquids on top of the instrument. Any spill into the ventilation openings could
cause electrical shock or damage to the instrument.
Biological Safety
• Empty the waste container when filling the sheath container or as needed to prevent leakage.
Take care to avoid damaging the fluid level sensor in the waste tank.
• Biological samples are potentially dangerous and/or life threatening. Adhere to proper
handling procedures for samples and reagents. Wear appropriate laboratory attire such as
protective gloves, eyewear, and lab coat.
• Any instrument surface in contact with biological specimens can transmit potentially fatal
disease. Use universal precautions when cleaning the instrument or replacing parts.
• Concentrations of sodium hypochlorite higher than 10%, as well as other cleaning agents can
damage the instrument.
Technical Support
For instrument support within the US, call 1-877-92-CYTEK. Visit our website, www.cytekbio.com,
for up-to-date contact information.
When contacting Cytek, have the following information available:
• Serial number
• Any error messages
• Details of recent performance

Chapter 2: Overview 9
2
Overview
Aurora System
The Aurora system consists of the Aurora flow cytometer and a computer workstation running
SpectroFlo™ software for acquisition and analysis. The system also includes SpectroFlo QC beads.
The cytometer is an air-cooled, compact benchtop instrument. It is equipped with three lasers and
up to 48 detection channels for fluorescence, and up to two detection channels for scatter (FSC and
violet laser SSC). Sheath and waste fluids are contained in either 4-L tanks or 20-L cubitainers.
During operation the software notifies you when the fluid levels are getting high or low. The
pressurized fluidics system includes a plenum for storing sheath, allowing you to fill and empty the
fluids during operation.
The workstation is a dedicated USB-compatible PC with monitor, keyboard, and mouse. It runs
Microsoft® Windows® 10 Pro 64-bit operating system, which is required for SpectroFlo software.
Figure 1. Aurora System

10 Aurora User’s Guide
Cytometer Overview
The Aurora spectral flow cytometer is an air-cooled, multi-laser, compact benchtop flow cytometer.
It is equipped with three lasers and up to 48 detection channels for fluorescence and up to two
detection channels for scatter (FSC [forward scatter] and violet laser SSC [side scatter]). Solid-state
lasers transmit light through a flow cell where particles in suspension are focused, single file for
interrogation by the laser. Proprietary, high-sensitivity, 16-channel semiconductor detector arrays
are equipped to capture the emission spectra of dyes that emit in the 400 to 900-nm wavelength
range. The resulting fluorescence and scatter are then collected and converted into electronic
signals. On-board electronics convert these signals into digital data that can be acquired and
recorded on the workstation.
The cytometer power button is located on the left side of the upper panel of the cytometer
(Figure 2). When the cytometer is powered on, the power button is illuminated.
The front panel opens on its hinges to the right to reveal the fluidics system. The top cover opens to
reveal the optics.
Front of Cytometer
Figure 2. Aurora front and left side panels
Do not place any object on top of the instrument.
Do not place liquids on top of the instrument. Fluid leaking into the cytometer could
cause electrical shock or damage to the instrument.
SIT door