Visium Spatial Gene Expression for FFPE
Common questions related to tissue preparation, assay workflow, sequencing, and analysis using FFPE tissues
General
- 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?
Tissue Preparation
- 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?
Staining
- 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)?
Imaging
Protocol Steps
- 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?
- Can I use an alternative to the KAPA SYBR Fast qPCR Master Mix (KK4600) for Cycle Number Determination during the Visium and Visium for FFPE Gene Expression workflows?
Transcriptome Probe Panels
- 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?
Sequencing
- 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?