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GeoMx

DSP

Instrument

User Manual

FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.

MAN-10152

-01

for v2.

software |

March

202

Summary of Contents for GeoMx DSP

Page 1: ...GeoMx DSP Instrument User Manual FOR RESEARCH USE ONLY Not for use in diagnostic procedures 2022 NanoString Technologies Inc All rights reserved MAN 10152 01 for v2 5 software March 2022...

Page 2: ...sales nanostring com EMEA europe sales nanostring com Asia Pacific Japan apac sales nanostring com Other Regions info nanostring com EU Authorized Representative NanoString Technologies Germany Gmbh...

Page 3: ...uotation NanoString grants you a limited non exclusive non transferable non sublicensable research use only license to use the proprietary GeoMx DSP System only in accordance with the manual and other...

Page 4: ...ty Information English 15 Consignes de S curit Fran ais 16 GeoMx DSP Workflow 17 User Manuals and Resources 19 GeoMx DSP Control Center 20 GeoMx DSP Run 21 Reagents and Consumables 21 Start a new run...

Page 5: ...and Scan Management 70 Administration Menu 74 GeoMx DSP Instrument Reagents 100 Changing Reagent Bottles 101 GeoMx DSP Instrument Maintenance 103 System Startup Shutdown 103 Cleaning the Slide Holder...

Page 6: ...DSP hibernation protocol for instruments that will be inactive for 2 weeks on page 106 l Added an Instrument Best Practices guide on page 110 l Added a Troubleshooting section on page 111 For NGS rea...

Page 7: ...ciency of the assay workflow IMPORTANT This symbol indicates important information that is critical to ensuring a successful assay Following these instructions may help improve the quality of your dat...

Page 8: ...l Spatial Profiler It is important that you read and comprehend the provided information Please utilize training resources in NanoString University at https university nanostring com and contact GeoMx...

Page 9: ...comes equipped with a 27 color LED monitor 4K 8MP model LG 27HJ712C W as well as a mouse and keyboard The front of the instrument has a USB port USB A 3 0 and a barcode scanner see Figure 2 The main...

Page 10: ...ll prompt you to slide the plate cover over the collection plate until loading is complete Up to four slides can be loaded into individual slots on the slide holder in a designated lab space each is s...

Page 11: ...addition the waste bottle with adequate space to collect waste must be present in the position to the right of the reagent bottles IMPORTANT Ensure the instrument is in an idle software state before c...

Page 12: ...connector l Three USB connections USB A 3 0 l A power input for the instrument Power in 100 240 VAC 50 60 Hz connector C14 l A power output for the monitor Power out same as Power in connector C13 l A...

Page 13: ...x D x H 30 in 760 cm W x 29 in 73 cm D x 24 in 61 cm H Power Requirements 100 240 VAC Fuse 50 60 Hz 10 A Room Temperature 18 28 C Room Humidity 30 80 relative humidity non condensing Table 1 GeoMx in...

Page 14: ...struction in this manual however some general safety guidelines are provided in Safety Information English on page 15 and in Disposal of Electronic Equipment on page 14 Product Use Limitations The Geo...

Page 15: ...s warranty Do not replace detachable main supply cords by inadequately rated cords WARNING Do not attempt to install move or perform maintenance on the instrument Always contact NanoString for instru...

Page 16: ...contacter NanoString pour instruction avant d installer ou le d placer l instrument S il est n cessaire de d placer l instrument utiliser une extr me prudence pour soulever des objets pesant plus de 2...

Page 17: ...formation Slides are scanned to capture fluorescent images used to select regions of interest ROIs The instrument collects UV cleaved oligos from the ROIs into the wells of a collection plate For NGS...

Page 18: ...Figure 6 GeoMx DSP workflow summary FOR RESEARCH USE ONLY Not for use in diagnostic procedures 18 GeoMx DSP Instrument User Manual GeoMx DSP Workflow MAN 10152 01 for software v2 5...

Page 19: ...r Manual MAN 10089 Workflow Step 4 GeoMx DSP Data Analysis User Manual MAN 10154 User manuals and other documents can be found online in the NanoString University Document Library at https university...

Page 20: ...r when Data Collection is selected provide you with a visual orientation of the progress of your run The Notifications bell will alert you to errors in archiving the status of readout file upload and...

Page 21: ...isted below you will need lint free wipes distilled water dH20 and 70 ethanol for cleaning the slides before the run GeoMx Instrument Buffer Kit GeoMx Slide Prep Kit only Buffer S is needed from this...

Page 22: ...ely and is not blocked by debris Use a lint free wipe and dH20 to clean the slide holder if needed See Cleaning the Slide Holder on page 105 for cleaning guidelines IMPORTANT Slide labels must not be...

Page 23: ...not extend beyond the gasket boundary l Clean the bottom of the slide again if needed with a lint free wipe and 70 ethanol IMPORTANT Ensure that there is no tissue slide label or other material betwe...

Page 24: ...esent run Collection will be set to use the next available well or row on the plate see details in Identify Plate on page 25 Open Close the Door Figure 12 Open the GeoMx instrument door when prompted...

Page 25: ...n the next available row of the plate If the previous collection was not finalized the same readout group must be used Collection will begin in the next available well of the plate unless the new coll...

Page 26: ...collection plate Figure 15 Cover the collection plate when prompted This prompt will appear if your collection plate was loaded before your slides Covering the collection plate see Figure 15 as you l...

Page 27: ...of the instrument see Figure 16 when prompted l Inspect visually and by touching to ensure that the slide holder fits evenly in the frame of the stage l The green slide numbers should be closest to t...

Page 28: ...the system will commence Slide Identification by taking a low magnification image of each loaded slide see Figure 17 Figure 17 Identify Slides stage in GeoMx DSP run workflow FOR RESEARCH USE ONLY Not...

Page 29: ...e Look Up button see Slide records on page 30 l Barcode This field auto populates with the slide record barcode if entered when linked to a slide record l Scan This contains the parameters for the sca...

Page 30: ...e information in the slide record l Click the Select Slide button Create l From the Identify Slides window select Create slide record l Open or create a new parent folder from the Navigation window l...

Page 31: ...n field or create a new set The collection of different analytes Protein and RNA on the same plate is not currently supported Do not run RNA and Protein slides in the same collection workflow 1 Enter...

Page 32: ...ill be available in the drop down Select the upload button to upload new configuration files from your USB drive if needed If newly uploaded files do not appear in the drop down exit the Scan Paramete...

Page 33: ...ets to an nCounter assay only one custom RNA module can be used per scan 3 Select the appropriate Scan Type and Focus Channel for your slide l The scan type option will be set to Fluorescence only l T...

Page 34: ...zoom movement on your touch screen or touch pad l Adjust the scan area using the X and Y sliders to define the area you would like to analyze l Use the Minimum Tissue slider to filter out particles f...

Page 35: ...l begin a high magnification scan of each slide using the defined tissue area and the scan parameters specified in the scan record see Figure 20 l Once the entire 20x scan is complete for a slide you...

Page 36: ...gram Once you have completed this process the GeoMx DSP instrument begins the collection of tags by exposing each segment of each ROI to UV light and aspirates material from the solution into a well o...

Page 37: ...Edit ROIs button see Figure 22 which will become active underneath a slide s image after the 20x scan has completed 2 To access the Scan Workspace from outside of the DSP run workflow select the Reco...

Page 38: ...ers date created and other details l Use the Full Screen control in the upper right corner of the scan image Zoom in and out using the scroll wheel on your mouse or a pinch zoom movement on your touch...

Page 39: ...rument damage Standard Geometric Shapes Figure 25 Scan Workspace square ROI button 1 Select a shape button circle or rectangle from the Scan Workspace see Figure 25 2 Click in the corner of the area y...

Page 40: ...turn to the polygon you wish to alter and it should resize properly 6 Each side of a polygon has a center point click on a center point to convert it to a vertex Click on a vertex to convert it to a c...

Page 41: ...nd drag The grid area will appear as a yellow dotted perimeter and the individual ROI previews will appear inside with white dotted line perimeters The ROI count within the grid will appear in the low...

Page 42: ...existing ROI Release the click to place the new ROI s l Select multiple ROIs by pressing Shift and then clicking the center of the desired ROIs l To delete the ROI s click the Delete or Backspace but...

Page 43: ...a for each ROI and any individual segments Nuclei that exist on the edge of two segments may be counted in both segments The displayed ROI area is calculated in micrometers whereas the segment area is...

Page 44: ...ignals are punctate An advanced approach to leveraging RNAscope with segmentation could be designed by leveraging the Image Overlay feature see Select ROIs on page 36 Practice Exercise to Establish Th...

Page 45: ...l l Increasing the Channel Thresholds number will increase the intensity required to be included in the segment and decrease the segment area l Decreasing the Channel Thresholds number will increase t...

Page 46: ...nt Definition one or more times to establish a definition for every segment you would like to create These segments will be applied across all ROIs Gray Segment Definition boxes will appear FOR RESEAR...

Page 47: ...rea on the scan if desired A default color will be present click on the color box to choose a different one l Delete a segment if desired 5 Segment generation order Use the grip bar to drag and drop s...

Page 48: ...7 Check the Show Advanced Parameters box to open Advanced Parameters see Figure 35 Here you can adjust numerous parameters including the order in which segments are generated and ultimately collected...

Page 49: ...y of generation order 8 After your first autosegmentation a Channel Thresholds grid will appear below your segment definitions allowing you adjust your segments manually for each ROI Adjust the values...

Page 50: ...l Use the Revert Thresholds button to revert to the default channel settings l Note that the collection order well order and name order of segments may differ from each other as the system optimizes a...

Page 51: ...ion and dimensions as the original exported TIFF Any pixel values greater than zero in your saved image will be treated as segment area Zero value pixels will be treated as empty space Return to the S...

Page 52: ...g and drop the gray overlay boxes to change the stacking order of the overlaid images 4 Click Alignment in the gray overlay box to reveal alignment tools on the scan see Figure 38 Alignment tools allo...

Page 53: ...38 2 Click Transfer to open the Select Scan window and select the scan from which to copy ROIs Click OK 3 The ROI Transfer process begins and progress is shown on the screen The time to transfer depe...

Page 54: ...age appears click Cancel or OK Any ROIs transferred to this scan will overwrite existing ROIs on this scan l If any ROIs are invalid the system will list them and give the option to cancel to realign...

Page 55: ...You may adjust these or add additional ROIs Figure 41 Scan Workspace ROIs Menu with segments 9 Any segment definitions existing in the source ROIs will transfer to the new scan To apply the transferre...

Page 56: ...well as an HTML summary of those images l Choose OME Tiff to export as a tiff file containing embedded OME XML metadata 3 Use the View ROIs and Overlays fields to indicate what to export on the scan l...

Page 57: ...ollection Save and Exit to save the ROIs without starting Collection at the current time The Scan Workspace will close and you will be returned to the slide view of your DSP run IMPORTANT DO NOT attem...

Page 58: ...does not automatically proceed following the plate change log out Ctrl Alt Del and log in again NOTE if placing a new plate for a collection with NGS readout do not swap to a plate that was previousl...

Page 59: ...these materials from the instrument without initiating a new run Removing the collection plate Figure 48 Unloading the collection plate Follow the prompts in the GeoMx DSP Control Center to remove the...

Page 60: ...in the instrument before shutting down or restarting If the door is locked click Assist wrench icon Restart Data Collection Workflow to reach the prompt to open the door 7 Follow the prompts to close...

Page 61: ...e used Collection will begin in the next available well of the plate unless the new collection is with a different kit configuration in which case it will begin in the next available row Different ana...

Page 62: ...on Readout Group window 1 Click Readout Group to see a list of available readout groups 2 Select the appropriate Illumina platform from the Counting Device Model menu 3 Choose Single or Paired Read 4...

Page 63: ...pace workgroup A notification that the run has been created appears in the Notifications bell Access through the BaseSpace Sequence Hub to start the run check progress and download results See Illumin...

Page 64: ...3000 4000 X l NovaSeq 6000 with v1 5 reagent kits l NextSeq 500 550 without local run manager sample sheet directly inputted into NextSeq 500 550 control software l NextSeq 1000 2000 set up with cust...

Page 65: ...the SampleID names in the SeqCodeIndices csv of the readout package l Make sure that there is a DCC file for every sample in the readout group For nCounter readout l Make sure there is not a folder wi...

Page 66: ...Select Save to save the new folder Figure 55 Records button and Navigation window Create a New Slide record 1 Select the Records button in the DSP Control Center 2 This will open the Navigation window...

Page 67: ...read No scans associated with this slide see Figure 56 To associate scan parameters with this slide record click the Add Scan button in the Slide Record window Figure 56 Slide record under Records in...

Page 68: ...e 59 GeoMx Melanoma TME Morphology Kit Human Figure 58 Example of GeoMx Melanoma TME Morphology scan parameters GeoMx Solid Tumor TME Morphology Kit Human Figure 59 Example of GeoMx Solid Tumor TME Mo...

Page 69: ...to all Selected Probe Kits listed on the right to remove them 3 Add the correct probe kits using the drop down menu on the left First select the Core Kit Then select any modules or custom kits If you...

Page 70: ...w Slide to create a new slide record l Select New Folder to create a new folder l Select a folder to view the slide records scan cards and studies within it Click on a folder icon to open close that f...

Page 71: ...ill inform on what stage it is in according to the GeoMx system l Defined scan is set up l Scanned scanning complete l Annotated ROIs selected l Aborted scanning or collection was aborted l Collection...

Page 72: ...in the upper left of the window see Figure 62 l Property Name l Constraint Contains l Value customizable field l Scan Order Scan Date Scan Name Slide Name Select Add Filter to apply a filter rule Appl...

Page 73: ...ed click the Add to Queue button to send this scan s counts to the Data Analysis queue See the GeoMx DSP Data Analysis User Manual MAN 10154 Editing or Deleting a folder Highlight a folder in the Navi...

Page 74: ...ss user and group accounts detailed below shutdown the instrument update the software download logs reset errors and warnings and access other system details see Figure 63 General users will only have...

Page 75: ...anoString personnel l ADMIN_RestoreSystemAfterWastePumpFlush xaml restores the DSP system into the right valve states and runs a script to make sure the waste pump has recovered from a previous proced...

Page 76: ...ow for Data Exchange study selection 2 Click on Data Exchange from the Administration menu Within the Data Exchange window navigate to the folder scan or study you d like to export see Figure 64 Use C...

Page 77: ...der into which you would like import 3 Once the desired folder has been highlighted click Import 4 View available external drives Select a drive Click Confirm Figure 66 Select Import File window 5 The...

Page 78: ...terrupt the download For best results do not navigate away until after the process is complete ERROR RESET An administrative user is able to access the error reset option through the Administration bu...

Page 79: ...h entered If including the domain use this format user domain l Password enter the correct password for the username Passwords may not include or or 2 Check the Archive Data box at the bottom of the f...

Page 80: ...uch as username username domain or username domain edu l Passwords may not have the characters l Confirm that the credentials to access the folder have reading and writing permission l Nested folders...

Page 81: ...sessions in progress will be terminated Note that the GeoMx Data Analysis Auxiliary Server software must be updated each time the paired GeoMx DSP instrument software is updated Figure 69 Auxiliary se...

Page 82: ...7 When the Setup Complete window appears click OK 8 The server availability and address will be displayed see Figure 70 If this information does not appear refresh the screen Ctrl R Figure 70 Auxiliar...

Page 83: ...a new Group Name and select Save RENAMING A GROUP 1 Once on the Group Management tab under Administration click the Rename button next to the group of interest 2 Enter the new name and select Save DE...

Page 84: ...button l To remove a user from the group highlight the individual in the Users in Group field and select the Remove Users button A confirmation message will appear select Save to complete the removal...

Page 85: ...on to a BaseSpace Workgroup 1 Access the GeoMx DSP over Chrome from a separate computer Log in as an administrative user 2 Click on the Administration menu then Illumina BaseSpace Admin 3 Click Add Co...

Page 86: ...umina com platform home apiKey list Figure 75 API Key List dialog l Click Generate to open the Generate an API Key dialog see Figure 76 Figure 76 Generate an API Key dialog l Enter a name for the key...

Page 87: ...s current workgroups Enterprise users navigate to https api EnterpriseURL v2 users current workgroups replace EnterpriseURL with the correct enterprise URL for your account If you are outside of the U...

Page 88: ...w nanostring com dspconfigfiles and transfer unzipped files to the instrument via USB Use the check boxes to activate or inactivate kit configuration files Only kits with checked boxes will be display...

Page 89: ...username and password 3 Select the Administration button in the DSP Control Center 4 From the Administration menu select Network 5 Note the Machine Name and the IP address listed in the Network Settin...

Page 90: ...t names and annotations Figure 80 Performance Monitoring option To turn on performance monitoring 1 Select Performance Monitoring from the Administration menu see Figure 80 2 Read the Terms and Agreem...

Page 91: ...PLATFORMS Use the Platform Selection window see Figure 81 to indicate the platforms your laboratory uses for GeoMx DSP data readout the nCounter platform Illumina NGS platform or both Figure 81 Platf...

Page 92: ...82 SSL certificate download 1 Login to the GeoMx system as an Administrative user Click on the Administration button and select the SSL Settings button from the menu 2 Click Download to download the s...

Page 93: ...dow 5 Click the Install Certificate button see Figure 84 Figure 85 Certificate import wizard local machine 6 Choose Local Machine and click Next see Figure 85 Administrative privileges are required fo...

Page 94: ...n tabs on Google Chrome then relaunch the browser You should now be able to connect to the GeoMx system remotely To do this browse to https geomx where is the GeoMx Machine Name find this information...

Page 95: ...considered to be in an idle state Replace Plate and Collection Complete If not already in an idle software state do the following 1 Click Data Collection then New Continue Run 2 Click Assist wrench ic...

Page 96: ...nto the GeoMx DSP system as an administrative user 2 From the Administration menu click on System Settings then System Time The System Time window will open see Figure 91 3 Check the box for Synchroni...

Page 97: ...sers to have more complex passwords With this box checked each user password created from this point forward must be at least 14 characters containing at least three of the following uppercase letter...

Page 98: ...Administrator or General general is default general users do not have access to most of the Administrative menu options In order to change a user s role Admin to User for example that user must be ass...

Page 99: ...DSP Control Center see Figure 94 Clicking on this symbol reveals any codes associated with the current state of the system If encountering a warning on your system contact GeoMxSupport nanostring com...

Page 100: ...the reagent bottles IMPORTANT Ensure the instrument is in an idle software state before changing reagents see Bring GeoMx DSP Software to an Idle Software State on page 95 In addition DO NOT top off a...

Page 101: ...e the reagent tray out for better accessibility 2 Remove the fitting from the bottle cap by pinching the dark gray button on the quick release with thumb and forefinger see Figure 96 Figure 96 Disconn...

Page 102: ...from the reagent bay holder see Figure 98 Figure 98 Removing GeoMx DSP waste 4 Unscrew and remove the cap assembly from the waste bottle 5 Empty the waste bottle 6 Rinse the waste bottle several time...

Page 103: ...the back of the instrument see Figure 99 Start Up 1 Switch the GeoMx DSP instrument power button to the On position The hardware will initialize homing and resetting positions as necessary 2 Once the...

Page 104: ...rmation Select OK to continue shutting down 5 A message will instruct you to allow 30 seconds before turning the physical power button to the off position Select OK to continue shutting down 6 A statu...

Page 105: ...Carefully replace gaskets to slide holder ensuring a good fit To minimize wear and tear on gaskets avoid frequent removal from the slide holder A brief cleaning following each instrument run should k...

Page 106: ...rform these steps without launching the Change Reagents wizard a Open the bottle bay door and unscrew the bottle cap assemblies from the Buffer S bottles in bottle slots 1 and 4 b Replace these two bo...

Page 107: ...gs then System Shutdown then Shutdown System c When the screen turns black after 30 seconds power off by flipping the switch on the back right of the instrument Return the system to operational 1 Swit...

Page 108: ...scan c When the high magnification scan is complete the system will initiate cleaning and move to the Collection Complete idlesoftware state d Once at the Collection Complete idle software state click...

Page 109: ...ICAL HAZARD Do not attempt to disassemble the instrument at any time An electric shock can occur if the instrument is operated without its outer case Properly shutdown then disconnect the instrument f...

Page 110: ...d disconnect and re secure QuickConnect cap fittings on all reagents and waste bottle l Upon start up log in and click Assist wrench icon then Restart Data Collection Workflow to bring the software to...

Page 111: ...ggested actions to resolve certain issues are listed below see Table 4 Issue Possible cause Suggested action Screen did not update or software is non responsive Lag in the user interface Click F5 on k...

Page 112: ...scan area impeding camera detection Confirm that tissue is within the Scan Area boundary shown in green see Figure 101 Scrape away excess hydrophobic pen residue if needed with a razor blade Load sli...

Page 113: ...area of slide or low volume of Buffer H or S Contact GeoMxSupport nanostring com to evaluate the situation This issue can often be prevented by examining slides to ensure that tissue does not exceed...

Page 114: ...nstrument I need to get my slides and plate out Error in run or time constraints Select Remove Slides and Microplate button if available Click Assist wrench icon Restart Data Collection Workflow then...

Page 115: ...European Community safety Safety CE Mark UK Conformity Assessed Mark Catalogue or Reference Number Batch code Lot number Serial number Temperature range storage conditions Lower limit of temperature s...

Page 116: ...om SALES CONTACTS United States us sales nanostring com EMEA europe sales nanostring com Asia Pacific Japan apac sales nanostring com Other regions info nanostring com CONTACT US info nanostring com T...

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