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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.
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. Symbol Meaning...
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 Aurora User’s Guide...
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).
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.
Figure 4. Sample injection port and sample injection tube Fluid Containers The Aurora draws sheath solution directly from a 20-L sheath cubitainer or the 4-L sheath tank provided by Cytek. It expels waste into an empty 20-L cubitainer or the 4-L waste tank provided by Cytek.
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Figure 5. Aurora fluidics bottles and front panel Fluid Flow The Aurora fluidics is driven by vacuum. An accumulator vessel is the source of vacuum for the system. Sheath solution is drawn into and stored in the sheath plenum before passing through a sheath filter where debris and contaminants are removed.
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Fluidics Components The following figure shows the fluidics components. Figure 7. Fluidics components (inside fluidics compartment) The following table describes the fluidics components. Component Description Plenum pump Pulls sheath from the sheath tank to fill the plenum Vacuum pump Maintains the vacuum in the accumulator Plenum Storage vessel for sheath fluid before it flows to the sheath filter Degasser...
Unlike conventional flow cytometers that direct specific bandwidths of fluorescence light into discrete detectors or photomultiplier tubes (PMTs), the Aurora uses a solid-state, multi-channel, narrow-beam detector array for each laser. Each array can be configured with up to 16 detectors that are used to capture a part of the emission spectrum from each particle passing through the laser beam.
Software Overview SpectroFlo software allows you to acquire and analyze samples and adjust instrument settings. Once you log into the software, a Get started menu appears with six modules from which to choose. Six options provide workspaces that allow you to perform various functions. Module Description QC &...
Single-stained controls must be acquired to calculate the amount of spillover into each of the non-primary detectors. The Aurora's ability to measure a fluorochrome’s full emission spectra allows the system to use a different method for isolating the desired signal from the unwanted signal. The key to differentiate the various fluorochromes is for those to have distinct patterns or signatures across the full spectrum.
Startup & Shutdown Filling the Sheath and Emptying the Waste The color-coded sheath and waste quick-connects and the waste level sensor connector are located at the lower-left corner of the front panel. sheath line quick-connect waste level sensor waste line quick-connect Figure 9.
Replace the waste cap/lid to the container. Hand-tighten the cap/lid until it is fully closed. Reattach the waste line and level sensor line to the cap/lid and front of the cytometer. If the cytometer is powered on and the software is connected, verify that the software waste indicator is green. Aurora User’s Guide...
Starting Up the System Turn on the workstation, then turn on cytometer. NOTE: Ensure that a tube of DI water is loaded on the SIP before launching SpectroFlo software. The tube is required for the SIT depth calibration. Launch SpectroFlo software and log in. The cytometer initialization procedure begins.
Leave the tube of DI water on the SIP. Make sure the SIT is submerged in the DI water at the end of the Fluidics Shutdown procedure. Exit SpectroFlo software by clicking the X in the upper-right corner of the application window. Turn off the cytometer and workstation. Aurora User’s Guide...
QC & Setup Daily QC Run Daily QC using SpectroFlo QC beads prior to acquiring samples to ensure that the cytometer is performing optimally. Daily QC assesses the instrument’s optical alignment and the system performance drift by measuring rCVs and gain needed to place the beads at the target locations for each detector.
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Different bead lots have different fluorescent intensities. Always select the correct bead lot when performing Daily QC. Select Start to begin the Daily QC run. The instrument begins acquiring the QC beads. The procedure takes approximately 3 to 5 minutes to complete. Aurora User’s Guide...
When Daily QC passes, the following message is displayed. You are now ready to acquire samples. QC Report At the completion of the Daily QC run, a QC report is generated. The report includes the following sections: • The header section contains the name of the instrument, date the Daily QC was run, user who ran the Daily QC, instrument configuration, instrument serial number, SpectroFlo QC bead lot and expiration date, and Pass/Fail status of the run.
Instrument Setup - Reference Controls Reference Controls must be acquired and recorded to ensure accurate spectral unmixing of the data. References are obtained by acquiring particles stained with individual fluorescent tags. Either beads or cells can be used as single-stained controls for acquiring references. You can select whether to create new Reference Controls or update Reference Controls already stored in the Library.
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0-10,000. If the positive population is off-scale for any detector channels, lower the gain setting for that channel. If the positive population is not sufficiently separated from the negative population within a specific channel, adjust the gain setting for that channel. Aurora User’s Guide...
NOTE: Dim markers may not separate from the negative population regardless of how much the gain is increased. Select Next when you are satisfied with the gain settings. Proceed to running controls. Running Reference Controls Once gain settings have been confirmed, unstained and Reference Controls are ready for acquisition.
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The gate can be selected manually. It is best to set the gate on the brightest emission as this can make distinguishing the positive and negative population easier. Readjust the positive and/or negative gate on the histogram, if necessary. Select Save to save the Reference Controls to the Library. Aurora User’s Guide...
Updating Reference Controls You may wish to update the Reference Controls if any of the following occur: • Major service performed on the instrument • Fluorochrome exhibiting signs of instability • Instrument exhibiting signs of instability The Reference Controls tab displays the Reference Controls saved in the Library. Click the arrow next to the control name to display the details.
You can set an alarm to warn you when the gain and %rCV exceeds the passing criteria that you define. This changes the outliers (shown in red) in the LJ graphs. Select Alarm Range from the Cytometer QC tab, then adjust the SD range (plus or minus) for individual detectors for each laser. Aurora User’s Guide...
Acquisition Raw vs Unmixed data SpectroFlo software saves flow cytometry data in the FCS 3.1 format. Data is saved in both raw and unmixed formats. Raw data contains all the fluorescence information from each detector. Each detector channel is designated by its excitation laser and position in the array. For example, B3 is the third channel of the blue laser detector array.
Change made to the default worksheet can be saved, however it is not recommended. Opens the New Experiment Wizard to guide you through creating an experiment. Template Allows you to select from a list of previously created templates. Import Imports template files that have been exported. Aurora User’s Guide...
Method Description My Experiments Allows you to select from a list of saved experiments. Experiments are organized into two categories—original (raw data) and unmixed. NOTE: Original experiments can be duplicated without data, which is equivalent to opening an experiment template. Experiment Display The experiment display in the Acquisition workspace includes the following panes: Sample List and Hierarchy...
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Count, Time Elapsed Events to Display Enter the number of events you want displayed during acquisition. Instrument Control The Instrument Control pane consists of the Gain, Threshold, Signal, and Lasers tabs for use in adjusting the instrument. Aurora User’s Guide...
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The following table describes the tabs in the Instrument Control pane. Description Gain Gains can be adjusted for all detector channels for all lasers using the gain spinboxes. FSC gain can be adjusted from 0–1,000. SSC and fluorescence detector gains can be adjusted from 0–10,000. To change the value that the gain increments, see the acquisition preferences on page 59.
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To change the properties of a plot, right-click the plot and select Plot Properties. You can select the plot type, parameters, scale, background color, and labels. Gates Gates types include: • rectangle • oval • polygon • quadrant • interval Aurora User’s Guide...
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The properties of gates can be changed by right-clicking the gate. You can change the name of the gate, the color, and gate boundary line weight. You can also select whether to display gates and statistics. Statistics To create a statistics box, click the Statistics icon in the experiment menu toolbar. Select the population checkbox next to the populations that have stats to display.
Creating a New Experiment With a Reference Group Select New in the Acquisition Experiment menu. The Create New Experiment wizard opens. Specify a name for the experiment and/or type in a description. Aurora User’s Guide...
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Select the fluorescent tags used in the experiment from the Library pane on the left. You must select all fluorescent tags present in the experiment, as this will determine which Reference Controls are to be used during spectral unmixing. NOTE: Use the search box in the upper-right corner of the Library pane to search for the fluorescent tags of choice.
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Select the control type for the single-stained Reference Controls. (Optional) Select the label that is conjugated to the fluorescent tag. Select Save. Aurora User’s Guide...
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Use the red trash can to delete one of the tubes from the Reference Group. This may be necessary if you wish to mix and match references acquired with stored Reference Controls. Any stored controls you plan to use should be deleted from the Reference Group. Once the Reference Group has been created, entries for each of the references will be displayed.
Multicolor samples can be acquired as raw data and unmixed post acquisition as well. This can be done either in the Acquisition workspace or in the Analysis workspace. Aurora User’s Guide...
Live Unmixing Samples can be unmixed during acquisition. Live unmixing can be performed with the Reference Group acquired during the experiment, the Reference Controls (run during QC & Setup and stored in the system), or a combination of both. For each sample tube that is live unmixed, two FCS files are generated, one that is composed of raw data and one that is composed of unmixed data.
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Negative to include the negative population. d. Select Live Unmixing. The wizard closes and the Acquisition workspace reappears. The Reference Group now has the unmixed icon to the left of the tube and a new unmixed worksheet appears. Aurora User’s Guide...
Post-Acquisition Unmixing Samples can be acquired as raw data and then unmixed after acquisition is complete in the experiment. This can be done through two methods: • post-acquisition unmixing in the Acquisition workspace • post-acquisition unmixing in the Analysis workspace Post-Acquisition Unmixing in the Acquisition workspace To perform post-acquisition unmixing in the Acquisition workspace, perform the same workflow as live unmixing EXCEPT the following:...
Advanced Unmixing Unmixing in the Analysis Workspace Post-acquisition unmixing with raw FCS files can be performed in the Acquisition workspace and can also be performed in the Analysis workspace. You can pick and choose which FCS files to unmix in the Analysis workspace (for example controls coming from different experiments or single- stained controls that were not run as part of the Reference Group).
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If the imported FCS files are incorrect, click Clear All to clear the entire imported list or select one or more FCS files to remove from the list and click Delete. FCS files designated as single-stained will require a fluorescent tag designation to specify what reference spectrum will be provided for unmixing. Aurora User’s Guide...
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Select Universal Negative for single-stained FCS files that do not contain a negative population. In the bottom left of the screen, check whether Auto Fluorescence will be used as a fluorescent tag. Select Refresh Plots to display the data in the FSC vs SSC plot, peak emission channel histogram, and spectrum plots.
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Preferences workspace. See “Storage” on page 65. Once unmixing is complete, the unmixed FCS files are saved in the specified directory. These FCS files can then be imported to an experiment for analysis or analyzed using third-party software. Aurora User’s Guide...
Virtual Filters Raw FCS data can be compensated using conventional methods in the Virtual Filter tab. Click the Virtual Filter tab in the Analysis workspace. Select Import to import raw FCS files for virtual filter analysis. These FCS files can be single-stained Reference Control FCS files, unstained control FCS files, and/or sample FCS files.
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To increase the bandwidth of the virtual filter, adjust the pull-down menus to capture the desired spectrum range. The following table shows the system’s filter bandwidths. Center Bandwidth Wavelength Wavelength End Laser Channel Wavelength (nm) (nm) Start (nm) (nm) Violet Blue Aurora User’s Guide...
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Select Show Plots to display the plots. The data is displayed in the FSC vs SSC plot and fluorescent tag histogram plot. The positive and negative populations need to be identified through the appropriate placement of the gates. a. Move the polygon gate in the FSC vs SSC plot to include the singlet population. b.
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Select Calculate Comp once gates have been set correctly. The conventionally compensated data is displayed in the Analysis workspace. The spillover matrix is also calculated and can be viewed under the Spillover matrix tab. Select Export to export the conventionally compensated data. Aurora User’s Guide...
Library, Preferences, and Users Library The Library contains information for various elements used for the experiments. Information saved in the Library includes SpectroFlo QC bead lots, fluorescent tags, labels, user settings, worksheet templates, and experiment templates. Information stored in the Library can be saved, exported, and imported for reuse.
The proteins that are either bound or attached to fluorescent tags can be designated as labels. The software comes with an initial set of pre-installed labels that are categorized as CD Markers, Chemokines, Chemokine Receptors, and Cytokines. Additional labels can be added by using Add in the right pane. Aurora User’s Guide...
New label groups can be created by clicking New. Label groups can also be imported and exported for use on other systems. The default labels can be edited but cannot be deleted. User Settings User Settings are the set of gain settings, threshold, and signal type for all detector channels. The name and description can be modified in this tab.
To view a worksheet, select View. Experiment Templates Experiment templates can be saved and stored in the Library. The name, creation date and time, description, and creator information is displayed. Experiment templates can also be imported and exported from this tab. Aurora User’s Guide...
Preferences The Preferences workspace allows you to change various functionality and display elements of the software user interface. The following section describes the options that can be changed in the Preferences workspace. Each section within the Preferences workspaces can be restored to its default settings by selecting Restore Default Preferences.
Grid Size – Modifies the size of the grid squares. Options include 1”, 1/2”, 1/4”, and 1/8”. Snap to Grid – Toggles on/off the ability for the worksheet elements to snap to and line up with the grid lines on the worksheet. Aurora User’s Guide...
Item Description Page Setup Show & Print Page Number – Toggles whether the page number is shown and printed. Print Header & Footer – Toggles whether the header and footer are printed. Print Grid Toggles whether the grid is printed. Can also be set to use Page Setting. Page Orientation Toggles between landscape and portrait.
Toggles on/off the display of the % of Parent with the gate name. together with Gate Name Show Count together Toggles on/off the display of the population count with the gate with Gate Name name. Gate Boundary Line Sets the thickness of the line drawn by the gate. Weight Aurora User’s Guide...
Item Description Interval Gate Default Toggles on/off whether the population captured by the interval gate Color has a default color. Quadrant Gate Default Select whether the population captured by the quadrant gate has a Color default color. Default Colors for First X Set the number of gates that will follow the color scheme detailed in Gates the gate color table.
Font Size – Select the font size. Color – Select the font color. Font Style – Toggles between normal and italic. Font Weight – Select normal, bold, or semibold. Sample Text Example preview text with the properties set in the Text Settings. Aurora User’s Guide...
Notifications The Notifications tab allows you to change certain notification settings in the Acquisition and Analysis workspaces. The following table describes the options in the Notifications preferences. Item Description Acquisition Module Toggles whether to display the Save Changes pop-up window when closing an Experiment, Worksheet, or User Settings.
The QC Setup tab allows you to select the days/months of QC reports to display in the Cytometer QC Reports menu. The following table describes the option in the QC Setup preferences. Item Description Display Daily QC Reports Select the number of Daily QC reports to be displayed in the Cytometer QC Reports menu. Aurora User’s Guide...
Users User accounts can be can be managed in the Users workspace. User account information and use time are stored in the workspace. There are two types of user accounts—administrator and operator. Only administrators can manage user accounts. Managing Users Administrators can add, remove, edit and disable user accounts from the User tab of the Users workspace.
(duration) for each user. To see the individual login sessions for each day, click Login Sessions. The log on and log off times for each session, as well as the session duration is displayed. Aurora User’s Guide...
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Chapter 7: Library, Preferences, and Users...
Use universal precautions when cleaning the instrument or replacing parts. Wear suitable protective clothing, eyewear, and gloves. Routine maintenance of the Aurora cytometer includes periodic replacement of parts. For part numbers, see “Supplies and Replacement Parts” on page 91.
In the Cytometer tab, from either the QC & Setup or Acquisition workspace, select Purge Filter. The vent valve connected to the sheath filter will open releasing any air bubbles trapped inside the sheath filter. Repeat the Purge Filter fluidic mode until there are no visible bubbles inside the sheath filter. Aurora User’s Guide...
Removing Air Bubbles from the Flow Cell Perform this procedure if the FSC and SSC signals appear abnormal. Air bubbles may be trapped in the flow cell, disrupting the sample flow. In the Cytometer tab, from either the QC & Setup or Acquisition workspace, select Degas Flow Cell.
Detach the sheath tank and replace it with a tank containing a 10% bleach solution. Install a tube containing 3 mL of a 10% bleach solution on the SIP. Proceed with the Long Clean in the software. Once the bleach cleaning cycle is complete, reattach the sheath tank. Aurora User’s Guide...
Remove the tube of 10% bleach from the SIP and replace with a tube of 3 mL of DI water. Proceed with the Long Clean in the software. When prompted, remove the long clean tubing assembly and re-install the sheath filter. Cleaning the External Surfaces Periodically check for saline residue.
NOTE: If the SIT is not protracted, turn on the cytometer and run Fluidics Shutdown. Then turn off the cytometer. Obtain a SIT tubing assembly. Open the SIT door. Identify the four components shown below. Aurora User’s Guide...
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The SIT door is located above the SIP. flow meter black plastic nut upper beige plastic nut Figure 12. Inside SIT door Twist off and carefully remove the black plastic nut from the bottom of the flow meter. Follow the tubing from the black nut down to the beige plastic nut. Twist off the beige nut and gently pull the beige nut and tubing out from the SIP.
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Verify that the tubing contacts the bottom of the tube on the SIP. If the end of the tubing is not positioned properly, ensure you performed steps 7 and 8. Aurora User’s Guide...
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Secure the black nut to the bottom of the flow meter. Turn the nut until it is firmly attached. Close the SIT door. Chapter 8: Maintenance...
This section provides tips to help you identify and resolve issues that might occur on your flow cytometer. If additional assistance is required, contact Cytek Biosciences. Please have the following information available: serial number, error messages, and details of recent performance.
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Run a Clean Flow Cell. Questionable sample prep Verify sample prep technique. Air in sheath filter Run a Purge Filter. Sample not diluted in same Dilute the sample in the same fluid as the fluid as sheath sheath solution. Aurora User’s Guide...
Glossary auto-fluorescence The inherent fluorescence arising primarily from cell structures such as mitochondria and lysosomes. Auto-fluorescence can hinder detection of dim fluorescent signals. compensation The process by which spillover fluorescence from secondary parameters is accounted for so that fluorescence values for a parameter represent only the fluorescence of the primary fluorophore.
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PMTs produce an output current proportional to the incident light intensity. Robust standard deviation. The robust SD is based on the deviation of individual data points to the median of the population. reference Spectral profile of a fluorescent tag in all detectors for all lasers. Aurora User’s Guide...
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resolution A measure of a cytometer's ability to distinguish between two populations with differing fluorescence or light scatter intensities. Sample injection port. The area of the cytometer where the sample is placed. Sample injection tube. The probe that pulls sample from the sample tube to the flow cell.
Forward and side scatter Enables separation of fixed platelets from noise. sensitivity Forward and side scatter Performance is optimized for resolving lymphocytes, monocytes, and resolution granulocytes, as well as microparticles. Side scatter resolution Capable of resolving 0.2-μm beads from noise. Aurora User’s Guide...
Supplies and Replacement Parts Item Part Number Description 4L Tank 60-30060-00 4-L tank for sheath or waste Lid for sheath tank 02-62001-00 Lid fits 4-L sheath tank and includes liquid level sensor. Lid for waste tank 02-62002-00 Lid fits 4-L waste tank and includes liquid level sensor. Cubitainer waste cap N7-32014-0A Cap fits 20-L waste cubitainer.
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