Questions & Answers
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SupportVisium
General
- Are the Visium slides charged?
- Are the Visium Spatial Tissue Optimization or Gene Expression slides re-usable if not all sections are used?
- Can different tissue types be tested on the Visium Spatial Gene Expression Slide?
- Can I modify the Visium Spatial Gene Expression solution to be targeted?
- Can I use the Visium Spatial Slide Reset Demonstrated Protocol to practice section placement for Visium?
- Do the spatial barcodes differ across individual capture areas on the Visium Spatial Gene Expression Slide?
Sample Preparation
- 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?
- Do I need to decontaminate the cryostat between different tissues types?
- How can I avoid overdrying of my tissue sections?
- Is there a maximum tissue section thickness?
Tissue Fixation and Staining
- Is the Visium with Immunofluorescence Demonstrated Protocol compatible with the Targeted Gene Expression assay?
- I have already optimized my antibodies for immunofluorescence on its own. Do I need to re-optimize my antibodies for the Visium with Immunofluorescence assay?
- How much time does the Visium with Immunofluorescence Demonstrated Protocol require?
- Does the Immunofluorescence portion of the 10x Demonstrated Protocol differ from standard Immunofluorescence protocols?
- Is my antibody compatible with the Visium Immunofluorescence (IF) Staining Demonstrated Protocol?
- What is the maximum number of antibodies that can be used with the demonstrated protocol for Visium with Immunofluorescence Staining ?
Imaging
- Does the etched frame on the Tissue Optimization slide need to be in-focus to interpret the experimental results?
- Can Visium Gene Expression Slides be stored post H&E staining?
- Does using a coverslip during imaging affect data quality?
- What are the imaging system requirements for running Visium?
- Is a color camera required for Hematoxylin & Eosin (H&E) imaging, or can a monochrome camera be used?
- What is the purpose of the Imaging Test Slide?
cDNA Quantification & Amplification
- Can I use an alternative to the KAPA SYBR Fast qPCR Master Mix (KK4600) for the cDNA cycle number determination step during the Visium Gene Expression workflow?
- 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?
- Where can I find the Dual Index Kit TT Set A (PN-1000215) sample index sequences?
- What is the structure of the final Visium library?
- What does a good Visium Spatial Gene Expression 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?
Sequencing
Software
- The fiducials are misaligned in my web summary — how can I fix this?
- How can I transfer pathologist annotations to Loupe Browser?
- TinyImageError: My image resolution is too low for Space Ranger. How can I fix it?
- Why is my Space Ranger run failing with manual alignment?
- Can I aggregate data from different samples or staining protocols using spaceranger aggr?
- How can I convert the feature-barcode matrix from Space Ranger 1.x to a CSV file?