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  1. 10X Genomics
  2. Visium Spatial Gene Expression for FFPE Assays
  3. Visium Spatial Gene Expression for FFPE

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?
See all 22 articles

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?
See all 25 articles

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)?
See all 16 articles

Imaging

  • What is the purpose of the Visium Spatial Imaging Test Slide for the Visium for FFPE v1 assay?
  • What can I do if the Fiducial Frame is dim during fluorescence imaging?
  • Why is coverslipping recommended for Visium for FFPE v1?
  • What are the imaging system requirements for running Visium for FFPE v1?

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?
See all 12 articles

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?
See all 6 articles

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?
See all 6 articles

Software

  • Where are the rest of the Visium for FFPE software articles?
  • How can I change spaceranger filtering for FFPE v1 probes?
  • Is my gene in the Visium for FFPE v1 probe set?
  • What is Visium Spatial Gene Expression for FFPE, and how does it work?
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