Visium CytAssist Gene and Protein Expression Library of Human Tonsil, H&E, 6.5 mm (FFPE)
CytAssist Spatial Gene and Protein Expression dataset analyzed using Space Ranger 2.1.0
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10x Genomics obtained a FFPE Human Tonsil tissue block from Avaden Biosciences. The tissue was sectioned as described in Visium CytAssist Spatial Gene and Protein Expression for FFPE – Tissue Preparation Guide (CG000660). 5 µm tissue sections were placed on Superfrost glass slides, deparaffinized, H&E stained (CG000658) and coverslipped. Sections were imaged, decoverslipped, followed by decrosslinking per the Staining Demonstrated Protocol (CG000658).
Sample Description:
- Sex: Female
- Age: 30s
The H&E image was acquired using Olympus Slide Scanning Microscope with these settings:
- Olympus Objective Magnification: 20X UPLXAPO Objective
- Numerical Aperture: 0.8
- ScopeLED light source: Xcite Novum
- Camera: Hamamatsu Orca FusionBT sCMOS
Libraries were prepared following the Visium CytAssist Spatial Gene and Protein Expression Reagent Kits User Guide (CG000494):
- Sequencing instrument: Illumina NovaSeq, flow cell H55KGDSX7 (lane 4)
- Sequencing depth (Gene): 35,000 reads per spot
- Sequencing depth (Protein): 20,000 reads per spot
- Sequencing configuration: 28bp read 1 (16bp Visium spatial barcode, 12bp UMI), 50bp read2 (probe insert/antibody barcode), 10bp i7 sample barcode and 10bp i5 sample barcode
- Dual-Index set: SI-TS-F9, SI-NT-F9
- Slide: V43J30-093
- Area: D1
Key metrics:
- Spots detected under tissue: 4,194
- Median genes per spot: 8,275
- Mean reads per spot: 111,046
- Mean Antibody reads per spot: 72,898
This dataset is licensed under the Creative Commons Attribution license.