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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 or Fresh Frozen tissues

General

  • How can I avoid mRNA degradation during the Visium CytAssist Spatial Gene Expression for Fresh Frozen (FF) assay?
  • How long does the Visium CytAssist Spatial Gene Expression for Fresh Frozen assay take to perform?
  • What tissue types have been validated with the Visium CytAssist Spatial Gene Expression for Fresh Frozen assay?
  • How should unused Visium CytAssist Spatial Gene Expression (v2) slides be stored?
  • Where are the validated stopping points in the Visium CytAssist Spatial Gene Expression for Fresh Frozen assay?
See all 29 articles

CytAssist Instrument

  • 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?
  • What are the Visium CytAssist camera specifications?
See all 28 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

  • How do I ship Tissue Slides once fresh frozen tissue sections have been placed?
  • How should I store tissue slides once fresh frozen tissue sections have been placed?
  • How should I prepare fresh tissue for shipment?
  • What section thickness is recommended for use with the Visium CytAssist for Fresh Frozen solution?
  • How should I prepare my fresh tissue for the Visium CytAssist Spatial Gene Expression for Fresh Frozen assay?

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

  • What tissue staining methods are compatible with the Visium CytAssist Spatial Gene Expression for Fresh Frozen assay?
  • Can staining methods other than H&E be used 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?
  • Is the Visium CytAssist Spatial Gene Expression for Fresh Frozen assay compatible with Immunofluorescence (IF) staining?

Imaging

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

Library Construction

  • Is it expected to have tissue remaining on the slide after CytAssist-enabled RNA Digestion & Tissue Removal? 
  • How do I assemble and disassemble the Visium Slide Cassette? 
  • Why does my Visium CytAssist Spatial Gene Expression library have additional, larger peaks in the trace?
  • 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 CytAssisted Visium Spatial Gene Expression assays 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

  • Visium for FFPE probe background signal
  • What is the Visium CytAssist instrument?
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