Questions & Answers
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SupportSpatial Gene Expression for FFPE
Probe-based assays allowing simultaneous analysis of molecular and imaging data from FFPE tissue sections.
General
General articles pertaining to Visium Spatial Gene Expression for FFPE
- Which thermal cyclers are compatible with the Visium for FFPE v1 assay?
- I'm using the Thermo Fisher Scientific Veriti© 96-Well Thermal Cycler (Cat No. 4375786) to run Visium, how should I set up the thermal cycler to maximize success?
- Are tissue microarrays (TMAs) supported with Visium for FFPE v1?
- My thermal cycler lid temperature doesn't go lower than 50°C, what should I do?
- Can I perform Spatial Gene Expression analysis using older FFPE blocks?
- What is the purpose of the Tissue Adhesion Test and how should it be performed?
Tissue Preparation
Content related to fixation, embedding, and information included in the Visium for FFPE Tissue Preparation Guide
- Is the Slide Reset Demonstrated Protocol (CG000332) compatible with the Visium Spatial Gene Expression for FFPE assay?
- How does over-fixation impact Visium for FFPE v1 assay performance?
- How are DV200% and Visium for FFPE assay performance correlated?
- Why does Visium for FFPE v1 call for DV200 as opposed to RIN evaluation for sample quality assessment?
- Why are there so many drying steps in the Visium for FFPE v1 Demonstrated Protocols?
- Should I punch and re-embed my FFPE block so my tissue can fit within the Capture Area?
Staining
Content related to the Visium for FFPE Staining Demonstrated Protocols
- Can I use Xylene alternatives for Deparaffinization with Visium for FFPE v1?
- How often should I refresh my deparaffinization and H&E staining solutions?
- How should I store the Gene Expression Slide after coverslip removal with Visium for FFPE?
- What steps can I take to minimize the impact of autofluorescence during immunofluorescence staining?
- Is Visium for FFPE compatible with immunohistochemistry (IHC)?
- How long is my FFPE tissue stable after coverslip removal?
Imaging
Imaging Visium Spatial Gene Expression for FFPE
Protocol Steps
Content related to steps detailed in the Visium Spatial Gene Expression for FFPE User Guide
- Why are the "Reads Mapped Confidently to the Probe Set" or "Reads Mapped Confidently to the Filtered Probe Set" metrics in my Spatial Gene Expression web summary file low?
- Why does my Visium Spatial Gene Expression for FFPE v1 library look unexpected or have low yield?
- Why is my Visium Spatial Gene Expression for FFPE v1 Cq value for Cycle Number Determination so high?
- How do I interpret the qPCR plot to determine the Sample Index PCR cycle number?
- During qPCR for Cycle Number Determination of the Visium and Visium for FFPE Gene Expression workflows, what should the real time controller lid temperature be set to?
- Can I use the Dual Index Kit Plate TT Set A, 96 rxns (PN-1000215) for Sample Index PCR with Visium for FFPE?
Transcriptome Probe Panels
Content related to probe design and performance
- Can I use PDX/xenograft tissue with Visium for FFPE?
- Can library molecules be generated from Probe Hybridization events with genomic DNA?
- If there is a mutation within the binding regions of two probes, will the probes still bind to the mRNA?
- What genes will not be detected by the Transcriptome Probe Panels?
- How were the Transcriptome Probe panels designed?
- How were the genes included in the Visium for FFPE v1 human probe set chosen?
Sequencing
Articles pertaining to sequencing Visium Spatial Gene Expression for FFPE libraries
- Can I perform shallow sequencing to assess the quality of Visium Spatial Gene Expression for FFPE libraries?
- Can Visium for FFPE libraries be pooled with other dual indexed 10x libraries?
- Where can I find the Dual Index Kit TS Set A sample index sequences?
- What is the suggested minimum sequencing depth for Visium for FFPE v1 libraries?
- What sequencers are Visium for FFPE v1 libraries compatible with?
- What are the recommended sequencing specifications for Visium for FFPE v1 libraries?
Software
Software articles specific to Visium for FFPE. Most Visium software articles live under the Visium for fresh-frozen Software section at https://kb.10xgenomics.com/hc/en-us/sections/360007318391-Software.