Questions & Answers
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SupportCytAssist 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
General articles pertaining to the Visium CytAssist Spatial Gene Expression solution
- How many freeze/thaw cycles are fine for Visium CytAssist Reagent Kit
- 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?
CytAssist Instrument
Frequently asked questions pertaining to the Visium CytAssist Instrument
- Are there additional resources to help troubleshoot network connectivity issues for the Visium 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?
Tissue Preparation - FFPE
Content related to fixation, embedding, sectioning included in the Visium CytAssist Spatial Gene Expression for FFPE - Tissue Preparation Guide
- 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?
- How do I determine if my tissue block or archived section will be compatible with the Visium CytAssist for FFPE assay?
Tissue Preparation - Fresh Frozen, Fixed Frozen
Content related to fixation, freezing, embedding, sectioning included in the Visium CytAssist Spatial Gene Expression for Fresh Frozen and Fixed Frozen - Tissue Preparation Guides
- What RNA extraction kits are compatible with Fixed Frozen samples?
- 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?
Tissue Staining - FFPE
Frequently asked questions related to the Visium CytAssist for FFPE Staining Demonstrated Protocols
- Can I use an autostainer with the Visium CytAssist FFPEv2 assay?
- Can I change the 60°C baking time during the deparaffinization step for my Visium FFPE samples?
- 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
Frequently asked questions related to the Visium CytAssist Spatial Gene Expression for Fresh Frozen or Fixed Frozen - H&E Staining Demonstrated Protocol
- 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?
- Is Immunofluorescence (IF) staining compatible with the Visium CytAssist Spatial Gene Expression for Fresh Frozen or Fixed Frozen assays?
Imaging
Frequently asked questions related to Imaging when performing the Visium CytAssist Spatial Gene Expression assay
Library Construction
Frequently asked questions related to steps detailed in the Visium CytAssist Spatial Gene Expression User Guide
- 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?
- What off-slide workflow steps are performed for generating Visium CytAssist Spatial Gene Expression libraries?
Transcriptome Probe Sets
Frequently asked questions related to probe design and performance with the Visium CytAssist Spatial Gene Expression solution
Sequencing
Frequently asked questions pertaining to sequencing Visium CytAssist Spatial Gene Expression libraries
- What is the recommended loading concentration of Visium CytAssist Spatial Gene and Protein Expression libraries on the NovaSeq 6000 Illumina sequencing platform?
- 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
Frequently asked questions specific to the Visium CytAssist Spatial Gene Expression solution