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  1. 10X Genomics
  2. Visium Spatial Gene Expression for FFPE Assays
  3. Visium CytAssist Spatial Gene Expression

Visium CytAssist Spatial Gene Expression

Common questions related to the Visium CytAssist instrument, tissue preparation, CytAssist-enabled assay workflow, sequencing, and analysis using FFPE, Fresh Frozen, or Fixed Frozen tissues

General

  • What tissue types have been validated with the Visium CytAssist Spatial Gene Expression for Fixed Frozen assay?
  • Where are the validated stopping points in the Visium CytAssist Spatial Gene Expression for Fixed Frozen assay?
  • How long does the Visium CytAssist Spatial Gene Expression for Fixed Frozen assay take to perform?
  • Is healthy bone compatible with the Visium CytAssist Spatial Gene Expression for FFPE assay?
  • Is healthy skin compatible with the Visium CytAssist Spatial Gene Expression for FFPE assay?
See all 33 articles

CytAssist Instrument

  • Why is my Visium CytAssist instrument not communicating with the 10x Cloud?
  • How do I set-up a Network Shared Folder on my Visium CytAssist?
  • How are images exported from the Visium CytAssist instrument?
  • What USB drive format is compatible with the Visium CytAssist instrument?
  • Is it expected for the corner back bumpers of my Visium CytAssist instrument to not touch the bench top?
See all 29 articles

Tissue Preparation - FFPE

  • How do I transport my tissue slide to another facility when tissue has already been placed?
  • How should I fix and embed my tissue for Visium CytAssist for FFPE?
  • How is tissue preparation similar and different between Visium for FFPE (v1) and Visium CytAssist for FFPE?
  • What key steps are similar and different when running archived, hard coverslipped slides as compared to freshly placed FFPE sections?
  • What section thickness would we recommend to use with the Visium CytAssist for FFPE solution?
See all 14 articles

Tissue Preparation - Fresh Frozen, Fixed Frozen

  • How should I prepare my tissue for the Visium CytAssist Spatial Gene Expression for Fixed Frozen assay?
  • How do I ship Tissue Slides once fresh frozen or fixed frozen tissue sections have been placed?
  • How should I store Tissue Slides once fresh frozen or fixed frozen tissue sections have been placed?
  • How should I prepare fresh tissue for shipment?
  • What tissue section thickness is recommended for use with the Visium CytAssist for Fresh Frozen and Fixed Frozen assays?
See all 6 articles

Tissue Staining - FFPE

  • Can I use Xylene alternatives when performing Tissue Deparaffinization during the Visium CytAssist for FFPE assay?
  • How do I assemble and disassemble the Visium CytAssist Tissue Slide Cassette?
  • How many antibodies have we simultaneously tested following the IF Staining Demonstrated Protocol for FFPE tissues?
  • Can I use a PAP pen instead of Tissue Slide Cassette when performing immunofluorescence staining?

Tissue Staining - Fresh Frozen, Fixed Frozen

  • Is Immunofluorescence (IF) staining compatible with Fixed Frozen mouse tissue samples?
  • What tissue staining methods are compatible with the Visium CytAssist Spatial Gene Expression for Fresh Frozen assay?
  • How are the tissue sections fixed to Tissue Slides during the Visium CytAssist Spatial Gene Expression for Fresh Frozen (FF) workflow?

Imaging

  • What are the general imaging system requirements for running Visium CytAssist Spatial Gene Expression assays?

Library Construction

  • Why does my Visium CytAssist Spatial Gene Expression library have an extra high molecular weight peak?
  • Is it expected to have tissue remaining on the Tissue Slides after CytAssist-enabled RNA Digestion & Tissue Removal? 
  • How do I assemble and disassemble the Visium Slide Cassette? 
  • What does a good Visium CytAssist Spatial Gene Expression library look like?
  • What’s the expected range of Cq values that should be obtained when performing the Cycle Number Determination step with the Visium CytAssist Spatial Gene Expression assays?
See all 9 articles

Transcriptome Probe Sets

  • How does the Human Transcriptome Probe Panel v2 differ from the Human Transcriptome Probe Panel v1?
  • How are the human probes used in the Visium CytAssist Spatial Gene Expression solution similar to and different from the probes used in the Fixed RNA Profiling solution?

Sequencing

  • Do the index sequences used for Visium CytAssist Spatial Gene Expression libraries overlap with other index plates?
  • Can Visium CytAssist Spatial Gene Expression libraries be pooled with other 10x libraries?
  • How do I determine how many spots are covered with tissue to determine sequencing depth needed?
  • What are the minimum recommended sequencing specifications for Visium CytAssist Spatial Gene Expression libraries?

Software Analysis

  • How to Add Custom Probes to Cell Ranger and Space Ranger
  • Can I combine data from Visium CytAssist for FFPE and Visium for FFPE (direct placement) if I am using the Mouse Transcriptome v1 probe set?
  • Visium FRP probe gDNA background signal
  • What is the Visium CytAssist instrument?
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