Visium CytAssist Gene and Protein Expression Library of Human Glioblastoma, IF, 11mm (FFPE)

10x Genomics obtained FFPE Human Glioblastoma 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, decrosslinked, IF stained, and coverslipped. Sections were imaged and decoverslipped per the Demonstrated Protocol (CG000659).

Sample Description:

• Sex: Female
• Age: 60s
• Date Excised: 2019
• DV200: 47.4

Antibodies used for immunofluorescence (IF) staining:

• Channel 1 = 1:200 DAPI (Thermo Fisher, Cat. No. 62248)
• Channel 2 = 1:100 PCNA, 594 nm, (Biolegend Cat. No. 307914 )
• Blocking buffer: 1X Blocking Buffer (10x Genomics Cat. No. 2000554); 2 U/uL RNase Inhibitor (10x Genomics Cat. No. 2000556)

The IF 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 H3TVGDSX7 (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-H11, SI-NT-H11
• Slide: V53J23-361
• Area: B1

Key metrics were:

• Spots detected under tissue: 5,756
• Median genes per spot: 7,629
• Mean reads per spot: 68,906
• Mean Antibody reads per spot: 75,377

This dataset is licensed under the Creative Commons Attribution license.