Human Ovarian Cancer, 11 mm Capture Area (FFPE)

10x Genomics obtained FFPE Human Ovarian Cancer tissue blocks from Avaden Biosciences. The tissue was sectioned as described in Visium CytAssist  Spatial Gene Expression for FFPE – Tissue Preparation Guide Demonstrated Protocol (CG000518). Tissue sections of 5 µm was placed on a standard glass slide,and H&E-stained following deparaffinization. After 11 months storage at room temperature, sections were imaged, decoverslipped, followed by deparaffinization steps, dehydration & Decrosslinking Demonstrated Protocol (CG000520). The glass slide with tissue section was processed via Visium CytAssist instrument to transfer analytes to a Visium CytAssist Spatial Gene Expression slide with 11 mm Capture Area. The probe extension and library construction steps follow the standard Visium for FFPE workflow outside of the instrument.

10x Genomics obtained FFPE Human Ovarian Cancer tissue blocks from Avaden Biosciences. The tissue was sectioned as described in Visium CytAssist  Spatial Gene Expression for FFPE – Tissue Preparation Guide Demonstrated Protocol (CG000518). Tissue sections of 5 µm was placed on a standard glass slide,and H&E-stained following deparaffinization. After 11 months storage at room temperature, sections were imaged, decoverslipped, followed by deparaffinization steps, dehydration & Decrosslinking Demonstrated Protocol (CG000520). The glass slide with tissue section was processed via Visium CytAssist instrument to transfer analytes to a Visium CytAssist Spatial Gene Expression slide with 11 mm Capture Area. The probe extension and library construction steps follow the standard Visium for FFPE workflow outside of the instrument.

• Diagnosis: Ovarian Serous Carcinoma, High Grade

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 Expression Reagent Kits for FFPE User Guide (CG000495).

• Sequencing instrument: Illumina NovaSeq, flow cell HNNN7DSX3 (lane 1-4)
• Sequencing depth: 46,109 reads per spot
• Sequencing configuration: 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-F4
• Slide: V52Y09-003
• Area: B1

Key metrics were:

• Spots detected under tissue: 4,674
• Median genes per spot: 8,792
• Median UMI counts per spot: 32,048

This dataset is licensed under the Creative Commons Attribution license.