Preservation Method Comparison on Visium CytAssist: FFPE Mouse Brain (Sagittal), 11 mm Capture Area

C57/Bl6 mice were obtained from Charles River Laboratory. Tissues were harvested from euthanized mice and formalin fixed and paraffin embedded. The tissue was sectioned as described in the Visium CytAssist Spatial Gene Expression for FFPE – Tissue Preparation Guide Demonstrated Protocol (CG000518). A tissue section of 5 µm was placed on a standard glass slide, and H&E-stained following deparaffinization and rehydration. The section was coverslipped with 85% glycerol, imaged, decoverslipped, followed by destaining and decrosslinking as described in Visium CytAssist Spatial Gene Expression for FFPE – Deparaffinization, H&E Staining, Imaging & Decrosslinking Demonstrated Protocol (CG000520). The glass slide with tissue section was processed with the Visium CytAssist instrument following the Visium CytAssist Spatial Gene Expression Reagent Kit User Guide (CG000495).

The H&E image was acquired using Olympus VS200 Slide Scanning Microscope with these settings:

• Olympus Objective magnification: 20x UPLXAPO Objective
• Numerical Aperture: 0.8
• ScopeLED light source: Xcite Novum
• Camera: VS-264C
• Exposure: 500 µs

Libraries were prepared following the Visium CytAssist Spatial Gene Expression Reagent Kit User Guide (CG000495).

• Sequencing instrument: Illumina NovaSeq 6, flow cell HLYH7DSX5 (lane 1-4)
• Sequencing configuration and coverage: 28bp read 1 (16bp Visium spatial barcode, 12bp UMI), 90bp read 2 (transcript), 10bp i7 sample barcode and 10bp i5 sample barcode
• Dual Index set: SI-TS-H12
• Slide: V52B25-081
• Capture Area: B

This dataset is licensed under the Creative Commons Attribution license.