10x Genomics 1000433 User Manual Download Page 48

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Summary of Contents for 1000433

Page 1: ... with Readiness Test For use with Visium CytAssist Accessory Kit 12 Month Warranty PN 1000441 Visium CytAssist Instrument Accessory Kit PN 1000433 Visium CytAssist Accessory Kit 24 Month Warranty PN 1000442 Visium CytAssist Instrument Accessory Kit PN 1000433 ...

Page 2: ...s may refer to the products or services offered by other companies by their brand name or company name solely for clarity and does not claim any rights in those third party marks or names 10x Genomics products may be covered by one or more of the patents as indicated at www 10xgenomics com patents The use of products described herein is subject to 10x Genomics Terms and Conditions of Sale availabl...

Page 3: ... CytAssist Instrument Document Revision Summary Link to TOC 10xgenomics com Document Revision Summary Document Number CG000542 Rev A Title Visium CytAssist Instrument User Guide with Readiness Test Revision Rev A Revision Date July 2022 ...

Page 4: ...ccessory Kits 13 Tips Best Practices 14 Icons 15 Check Tissue Placement on Slide 15 Tissue Slide Placement on Tissue Slide Stage 17 Visium Slide Placement on Visium Slide Stage 22 10x Genomics Cloud 23 Menu Options 24 Menu Options 25 Firmware Update Procedure 28 System Operation 30 Step 1 Installation 31 Step 2 First Time Use 33 Step 3 Readiness Test 36 Step 4 Main Operation 38 Maintenance 42 Syst...

Page 5: ...Introduction 6 Introduction 7 Product Identification 7 Product Specifications ...

Page 6: ...tions can be captured on CytAssist specific slides in less than one hour per run Highlights Simplify sample handling with automated transfer of transcriptomic analytes from standard slides onto the Capture Area of a Visium slide Eliminate the need to section directly onto the Visium slide and expand sample compatibility to pre sectioned slides Maximize insights from Visium experiments by pre scree...

Page 7: ... the sensitive reagents used with the instrument Humidity 30 80 R H non condensing Power Cable Length Power cables will be in accordance with regional specifications 6 7 ft 2 m Standard Product Specifications 9 76 8 12 3 13 1 max height 10X GENOMICS INC 2020 CONFIDENTIAL DO NOT DISTRIBUTE Visium CytAssist LBL 00042 01 Regulatory Label Must be legible from 18 inches Electrical shock warning require...

Page 8: ...Safety Compliance Information 9 Safety 10 Regulatory ...

Page 9: ...the presence of moving mechanical parts that can be harmful to the operator if handled incorrectly The Hazardous Materials symbol indicates the presence of materials that are toxic or otherwise harmful to the operator if handled incorrectly The Biohazard symbol indicates the presence of biological samples that can be harmful to the operator if handled incorrectly Ensure ground is reliably connecte...

Page 10: ...vironment EN 61000 3 2 Electromagnetic compatibility EMC Part 3 2 Limits Limits for harmonic current emissions equipment input current 16 A per phase EN 61000 3 3 Electromagnetic compatibility EMC Part 3 3 Limits Limitation of voltage changes voltage fluctuations and flicker in public low voltage supply systems for equipment with rated current 16 A per phase and not subject to conditional connecti...

Page 11: ...System Components 12 System Components 13 Accessory Kits ...

Page 12: ... Shipping Bolt Secures the camera during transportation removed during installation Interior Tissue Slide Stage Tissue Slide Clips Slide Alignment Guides Visium Slide Lock Visium Slide Stage Tissue Alignment Windows Visium Alignment Windows Exterior USB Port Touchscreen Lid Handle Base Adjustable Feet Corner Bumper Corner Bumper Non adjustable Back Foot ...

Page 13: ...Cards for Accessory Kit Instruction 1 CG000548 Visium CytAssist Training Kit 1 1000458 Visium CytAssist Training Slide Assembly 2 2000681 Blank Slides 2 3000868 Visium CytAssist Calibration Kit 1 1000459 Visium CytAssist Calibration Slide Assembly 1 2000680 Blank Slides 2 3000868 Product Part Number Item Shipping Bolt Located in the back of the instrument during transportation removed during insta...

Page 14: ...Tips Best Practices 15 Icons 15 Check Tissue Placement on Slide 17 Tissue Slide Placement on Tissue Slide Stage 20 Visium Slide Placement on Visium Slide Stage 21 10x Genomics Cloud ...

Page 15: ...0548 located within the Instrument Accessory Kit laminated document with concise instructions a Ensure that the tissue region of interest will fit within the Capture Area of a Visium CytAssist Spatial Gene Expression Slide Overlay the slide centering the tissue on either the 6 5 mm or 11 mm square b If the slide has no frosted areas overlay on this diagram The tissue should lie within the green al...

Page 16: ...e tissue lies within the green allowable area 15 mm from edge of frosted area marks 5 mm from the sides c Refer to the examples of good and bad tissue placement Refer to the Visium CytAssist Training Kit User Guide CG000549 for further guidance If printing this page Select actual size or 100 to print to scale The slide diagrams should each measure 25 mm wide Examples of Good Tissue Placement Blank...

Page 17: ... center of the alignment guides for 6 5 mm rectangles or 11 mm lines Capture Areas on either the left or right side of the stage Align the center of the tissue region of interest to the center of the Capture Area rather than aligning the edge of the region to the edge of the Capture Area If printing this page Select actual size or 100 to print to scale The blue Capture Area should measure 11 mm an...

Page 18: ...ermost position Examples of Good Slide Placement on the Tissue Slide Stage right side of the stage rotated still on the right side of the stage OR F F Slide F shown with a 6 5 mm section left side of the stage OR rotated still on the left side of the stage G G Slide G shown with a 11 mm section Tissue Slide Placement on Tissue Slide Stage contd Overlay of a 11 mm fiducial frame and the alignment g...

Page 19: ... adjust the position of the tissue within the alignment guides DO NOT touch the tissue section d If only one tissue on one slide will be loaded use a blank slide for the second position on the Tissue Slide Stage B C Secure slide Pivot clip Tissue Slide Placement on Tissue Slide Stage contd CORRECT Tissue lies completely within alignment guides INCORRECT Tissue is intersected by alignment guides 6 ...

Page 20: ...ring that the slide is not impacted The lock will partially obscure the slide label when correctly secured Visium Slide Stage is Empty Visium Slide Stage is Loaded Correctly with One Slide CORRECT Slide fits inside the grooves Label on the right is partially obscured by the lock Capture Areas line up with alignment windows INCORRECT Slide does not fit inside the grooves Capture Areas do not line u...

Page 21: ...s com The image below demonstrates how movement of the tissue slides affects where target molecules will end up on the Visium CytAssist Spatial Gene Expression Slide Stage Tissue Slide Visium Slide POSITION OF TISSUE ON TISSUE SLIDE STAGE RESULTING POSITION OF TARGET MOLECULES ON VISIUM SLIDE ...

Page 22: ...de Stage a Inspect the Visium Slide Stage for dust and debris and clean according to the Maintenance section as needed b Open the Visium Slide Lock by using one finger to pivot c Line up the slide with the label face up and oriented to the right d Fit the slide within the raised grooves on the left top and bottom Visium Slide Placement on Visium Slide Stage Visium CytAssist Spatial Gene Expression...

Page 23: ...nstrument information and download the latest firmware updates for their instruments Each Visium CytAssist instrument is required to be registered to the 10x Genomics Cloud during the First Time Use FTU set up process Users may register multiple instruments to their accounts and each instrument can optionally be registered to multiple 10x Genomics accounts Instruments connected to the network can ...

Page 24: ...Menu Options 23 Menu Options 26 Firmware Update Procedure ...

Page 25: ...ument section Instrument Data Fromthismenuoption accessandexport Run Data includes CytAssist images run csv with metadata such as sample run name slide serial number etc Size 10s of mb run Support Package includes Run Data plus instrument telemetry and sensor information captured both during instrument run and instrument idle time Size 100s of mb run ShareSupportPackagewith10xGenomicsTechnicalSupp...

Page 26: ...n while older Support Data is deleted automatically oldest files are deleted first It is critical that users proceed to the next stage of the workflow in the assay kit user guide immediately rather than exporting data right away Export Procedure a Click the Download button on the home screen b Insert a USB Onscreen select the USB destination for exported data c Select runs for export then click St...

Page 27: ...recommended so that the instrument may receive security firmware updates and automatically upload system log files to the 10x Genomics Cloud 10x Genomics has no remote access to the instrument Users may separately configure connectivity settings related to firmware updates and log upload behavior Network Security Allow the following outbound ports for 10x Genomics Cloud access TCP port 443 As an a...

Page 28: ...oad enabled e A pop up on the home screen will alert the user of available updates f Open pop up and click to install Procedure with a network connection auto download disabled a A pop up on the home screen will alert the user of available updates b Open pop up and click to download c Click to install Procedure with no network connection a Visit cloud 10xgenomics com to view firmware updates b Dow...

Page 29: ...n to start the test e Upon test completion follow onscreen instruction to unload slides Follow onscreen instruction in the event of a failed or incomplete test f Store the blank slides and the calibration slide in their original packaging bag away from sunlight and extreme temperature Retain for future use g Wipe down the Tissue Slide Stage and the Visium Slide Stage with 70 ethanol or 70 isopropa...

Page 30: ...System Operation 29 Step 1 Installation 31 Step 2 First Time Use 34 Step 3 Readiness Test 36 Step 4 Main Operation ...

Page 31: ...he instrument Provides a minimum of 4 10 cm clearance around unit to allow free air circulation Warning Avoid using the Visium CytAssist in a manner not specified by 10x Genomics The Visium CytAssist has been designed to protect the user If used improperly the intended user protections can be impaired General Power Safety Grounding is required to prevent electric shock If the power source is not g...

Page 32: ...see Moving Shipping the Instrument section d Remove Shipping Bolt from the back of the instrument Retain for future use the Shipping Bolt holds the camera focus in a safe position during transportation e Open lid Carefully remove tape from the four Tissue Slide Clips and the Visium Slide Lock as well as from the opposite end f Remove glass protective films from the alignment windows on both stages...

Page 33: ...uires the following 10x Genomics Account Onscreen instruction will guide account setup Alternatively visit cloud 10xgenomics com to create an account beforehand Instrument serial number and instrument ID Located onscreen during setup and also on the label at the back of the instrument Network settings A computer with Internet access Internet connection to the instrument is highly recommended Note ...

Page 34: ...d accept the legal agreement e Update the firmware Internet connection After registration the instrument will automatically search for the latest firmware update Confirm data transmission settings for automatic upload download No Internet connection Download the latest firmware update from your 10x Genomics account to the USB provided in the Instrument Accessory Kit Insert USB into the back of the...

Page 35: ...r increasing height The feet will come off the instrument if they are continued to be turned counterclockwise Once the instrument is leveled correctly check the back of the instrument to confirm that the center back non adjustable foot is resting on the table top while the two non adjustable corner back bumpers are not touching the table top See Troubleshooting section if an error occurs during th...

Page 36: ...on Slide in the Instrument Accessory Kit Inspect for any chips or cracks Calibration slide may be cleaned with lens paper or laboratory wipes followed by compressed air Dirty slides may cause the readiness test to fail c Enter the serial number on the calibration slide using a different serial number could result in poor calibration d Open the instrument lid e Follow onscreen instruction and load ...

Page 37: ...ollowed by 70 ethanol or 70 isopropanol Use compressed air to dry remove debris as needed Clean glass windows with dry polyester swabs such as Texwipe TX714A Cleanroom Swab 0 5 L EW 33677 62 from Cole Parmer or equivalent and compressed air Use a bright light e g flashlight to inspect the glass windows for any smudges and remove them as described above k Close the lid clicking sound indicates clos...

Page 38: ...n area that results in successful analyte transfer and imaging Overlay the slides on the diagrams in the Visium CytAssist Quick Reference Cards for Accessory Kit Instruction CG000548 located in the Instrument Accessory Kit Refer to the Tips Best Practices section for further guidance If only one tissue on one slide will be loaded use a blank slide for the second position on the Tissue Slide Stage ...

Page 39: ...A and B c Open lid d Follow onscreen instruction and load the blank slides and calibration slide onto the instrument as described in the Tips and Best Practices section e Load reagents to the circular dispensing well on each spacer when instructed in the appropriate assay kit user guide be mindful of time sensitive reagents f Close the lid clicking sound indicates closure Pinch risk Ensure no obst...

Page 40: ...Done and a Run Info tab at the bottom of the screen Green indicates a successfully completed run Red indicates a failed run error see Troubleshooting Yellow indicates that the run has been canceled i Click the Done button and open lid DO NOT power off the instrument at this time as it needs to process support data j IMMEDIATELY remove the Visium CytAssist slide from the instrument and proceed with...

Page 41: ...ry run See Maintenance section for further guidance l Export the run data via USB See Run Data section for further guidance m View and verify the tissue samples were accurately aligned within the Visium CytAssist Slide fiducial frame See the relevant assay kit user guide for further guidance The instrument requires a 20 min cool down between runs Step 4 Main Operation contd ...

Page 42: ...Maintenance 41 System Maintenance 43 Moving Shipping the Instrument ...

Page 43: ...exwipe TX714A Cleanroom Swab 0 5 L EW 33677 62 from Cole Parmer or equivalent and compressed air Use a bright light e g flashlight to inspect the glass windows for any smudges and remove them as described above d Close the lid clicking sound indicates closure Wipe down the base and lid of the instrument See System Components section for interior and exterior images Interior The Visium Slide Stage ...

Page 44: ...ist has been damaged in any way e g a power entry module or plug is damaged liquid was spilled into or objects fell into the instrument the instrument does not operate properly or has been dropped Use only the power cord supplied with the Visium CytAssist Do not replace it with a non approved power cord as it may be inadequately rated to handle the electrical loads If replacing the externally acce...

Page 45: ...nstrument transportation Menu Options System Alternate Modes Shipping Mode b Once Shipping Mode is active follow onscreen instruction to power down the instrument c Turn off the instrument completely using the power switch on the back of the instrument d Remove the power cord e Decontaminate the instrument see System Maintenance section Step 2 Packaging Instructions a Fully tighten the two adjusta...

Page 46: ...ve the four Tissue Clips to their innermost positions and tape down Ensure that the tape is placed over all four Tissue Slide Clips along with the overlap with all four corners of the protective film f Close lid Apply laboratory labeling tape to one side of the base across the top of the lid and down the other side of the base prevents the lid from opening during transport Apply glass protective f...

Page 47: ...s Place the foam packaging on top of the instrument i Unless directed otherwise do not include any parts of the Accessory Kit which includes the power cord j Coordinate with 10x Genomics Support for further return instructions some required paperwork will be placed in the box Place the required documents into the box k Seal the box and apply the shipping label l The instrument is now ready for tra...

Page 48: ...Troubleshooting 47 Troubleshooting 49 Error Screens ...

Page 49: ...ar tissue on tissue slide if bubbles are outside of the tissue the risk of affecting assay performance is low If bubbles are on top of the tissue it may result in lack of usable reads in the tissue area with the bubble Best practice ensure reagent is prepared properly and correctly dispensed to the wells to avoid introducing bubbles Visium Slide Popped out of the Grooves Debris on the Slide Stage ...

Page 50: ...User Guide CG000549 Readiness Test Fails Refer to the Maintenance section and clean the instrument as described Wipe down the Tissue Slide Stage and the Visium Slide Stage with 5 10 bleach solution followed by 70 ethanol or 70 isopropanol Use compressed air to dry and remove debris as needed Clean glass windows with dry polyester swabs such as Texwipe TX714A Cleanroom Swab 0 5 L EW 33677 62 from C...

Page 51: ...les for troubleshooting Upload pertinent logs to 10x Genomics by navigating to the Logs menu option on screen See Run Data section There are two types of errors Critical Errors When the instrument has seen a critical error the run will immediately abort Do not proceed with any further runs Contact support 10xgenomics com with the error code System Error Run Error Canceled User Recoverable Errors F...

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