Questions & Answers
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Poly-A based assay allowing simultaneous analysis of molecular and imaging data from fresh frozen tissue sections.
General
- Are the Visium slides charged?
- Are the Visium Spatial Tissue Optimization or Gene Expression slides re-usable if not all sections are used?
- At what step in the workflow can I use the Visium Spatial Slide Reset Demonstrated Protocol?
- Can I modify the Visium for fresh-frozen Spatial Gene Expression solution to be targeted?
- Can I run different tissue types on a single Visium Spatial Gene Expression Slide for the Visium for fresh-frozen assay?
- Can I use different permeabilization time points on a single Visium Gene Expression slide?
Sample Preparation
- Are fresh-frozen tissues containing bone compatible with Visium Spatial Gene Expression?
- Can I perform both Single Cell Gene Expression and Visium Spatial Gene Expression experiments on my OCT-embedded tissue block?
- Can OCT affect bulk RNA extraction and RIN assessment?
- How can I more easily visualize the fiducial frame during tissue section placement?
- Can I section from the same tissue block across multiple days?
- Can OCT cover the Fiducial Frame or extend outside the capture area?
Tissue Fixation and Staining
- I have already optimized my antibodies for immunofluorescence on its own. Do I need to re-optimize my antibodies for the Visium for fresh-frozen Immunofluorescence assay?
- How much time does the Immunofluorescence Staining Demonstrated Protocol for Visium for fresh-frozen require?
- Does the Visium for fresh-frozen Immunofluorescence Demonstrated Protocol differ from standard immunofluorescence protocols?
- Is my antibody compatible with the Visium for fresh-frozen Immunofluorescence (IF) Staining Demonstrated Protocol?
- What is the maximum number of antibodies that can be used when performing Visium with Immunofluorescence?
- What tissue types have been validated with the Visium for fresh-frozen Immunofluorescence Demonstrated Protocol?
Imaging
- Can Visium Spatial Gene Expression Slides be stored post-Immunofluorescence staining?
- Does the etched frame on the Tissue Optimization slide need to be in-focus to interpret the experimental results?
- Can Visium Spatial Gene Expression Slides be stored post H&E staining?
- Does using a coverslip during imaging affect Visium for fresh-frozen data quality?
- What are the imaging system requirements for running Visium for fresh-frozen?
- Is a color camera required for Hematoxylin & Eosin (H&E) imaging, or can a monochrome camera be used?
cDNA Quantification & Amplification
- How do I interpret the qPCR plot to determine the cDNA amplification cycle number?
- Can I use an alternative to the KAPA SYBR Fast qPCR Master Mix for Cycle Number Determination during the Visium Gene Expression workflows?
- Can I use alternative methods to qPCR such as Nanodrop or Qubit for cDNA quantification during the Visium Gene Expression workflow?
- Which qPCR systems can be used for the Visium assay?
Library Construction
- Why were the Sample Index PCR conditions updated for Visium Spatial Gene Expression library preparation?
- What is the structure of the final Visium for fresh-frozen library?
- What does a good Visium Spatial Gene Expression for fresh-frozen library look like?
- Can I use the Chromium i7 Multiplex Plate (PN-2201013) for Sample Index PCR with Visium?
- What sample index plate is required for performing Sample Index PCR with Visium for fresh-frozen?
Sequencing
- Can I perform shallow sequencing to assess the quality of Visium Spatial Gene Expression for Fresh Frozen libraries?
- Can I use a 100-cycle NovaSeq 6000 kit to sequence Visium libraries?
- Why do a fraction of my Visium reads contain the Template Switch Oligo (TSO) at the beginning of Read 2?
- Where can I find the Dual Index Kit TT Set A (PN-1000215) sample index sequences?
- Can Visium for fresh-frozen libraries be pooled with other 10x libraries?
- What sequencing parameters should be used for Visium for fresh-frozen libraries?
Software
Software for the Visium Solution
- Why do my Visium CytAssist samples have poor mapping metrics?
- Why did Space Ranger fail to correctly align the CytAssist image with the high resolution microscope image?
- How should I annotate the topics from reference free spot deconvolution?
- Is reference-free spot deconvolution better than reference guided spot deconvolution?
- Can I align my H&E image and IF stained images to each other using Loupe Browser for my Visium data?
- What is the Median Normalized Average statistic in Loupe Browser in the Moran's I table?