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?
• Do the spatial barcodes differ across individual capture areas on the Visium Spatial Gene Expression Slide?
• Do we recommend replicates for Visium Gene Expression slides?

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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?

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Tissue Fixation and Staining

• Can the H&E staining process have a negative impact on RNA integrity and reduce assay sensitivity?
• Can staining methods other than H&E be used with the Visium Solution?
• Is Visium compatible with cells or tissues expressing a reporter allele such as GFP?
• How are the tissue sections fixed to the capture areas on the Visium slide?

Imaging

• 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 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

• 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 index plate do I need for performing sample index PCR with Visium?
• What sequencing parameters should be used for Visium libraries?

Sequencing

• Can Visium libraries be pooled with other 10x libraries?
• What are the minimum recommended sequencing specifications for Visium libraries?
• Can I change the sequencing read lengths of the i5 and i7 indices?
• What sequencers are Visium libraries compatible with?

Software

• How can I convert the feature-barcode matrix from Space Ranger 1.x to a CSV file?
• Can I manually mark spots covered by tissue in my Visium experiment?
• Where can I find the Space Ranger barcode whitelist and their coordinates on the slide?
• How do I use the Loupe Browser to estimate the number of tissue covered spots in my Visium sample?
• Can I use spaceranger mkfastq to demultiplex my data if I sequenced 8bp of the index reads instead of 10?
• Can Space Ranger and Loupe be used to analyze data from the product developed by Spatial Transcriptomics before 10x acquired it?