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?
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?
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?
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
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?
Transcriptome Probe Sets
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?