Visium CytAssist Gene and Protein Expression Library of Human Tonsil, H&E, 6.5 mm (FFPE)

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.