Cross-Platform Comparison: FF Human Ovarian Cancer with Xenium v1 and Xenium Prime 5K

Overview

These datasets are from adjacent tissue sections:

• Xenium v1 In Situ Gene Expression with Cell Segmentation data for human ovarian cancer (FF) using the Xenium Human Multi-Tissue and Cancer Panel plus 100 custom genes.
• Xenium Prime 5K In Situ Gene Expression with Cell Segmentation data for human ovarian cancer (FF) using the Xenium Prime 5K Human Pan Tissue and Pathways Panel.

The Visium HD and HD 3' Spatial Gene Expression datasets that were generated from tissue sections adjacent to those for the Xenium In Situ datasets are available here:

• Visium HD ovarian cancer, sequencing depth comparison
• Visium HD 3' ovarian cancer, sequencing depth comparison

How to view data

Interactively explore data with Xenium Explorer by downloading the Xenium Output Bundle (or Xenium Explorer subset) file. The subset bundle contains the experiment.xenium, gene_panel.json, morphology_focus/ directory of multi-file OME-TIFF files, analysis_summary.html, cells.zarr.zip, cell_feature_matrix.zarr.zip, transcripts.zarr.zip, and analysis.zarr.zip files.

See the Getting Started with Xenium Explorer page for more details. Follow these instructions to view the post-Xenium H&E image or image alignment file in Xenium Explorer.

Biomaterials

Fresh frozen tissue was purchased from Discovery Life Sciences prior to in-house embedding in OCT (Ovarian Cancer, Ovarian Papillary Serous Carcinoma, II-A).

Tissue preparation

Tissues were prepared following the Xenium In Situ - Fresh Frozen Tissue Preparation Handbook (CG000579).

• Xenium v1 sample: Probe hybridization, washing, ligation, amplification, and cell segmentation staining were performed following the Xenium In Situ Gene Expression with Cell Segmentation Staining User Guide (CG000749).
• Xenium Prime 5K sample: Probe hybridization, washing, ligation, amplification, and cell segmentation staining were performed following the Xenium Prime In Situ Gene Expression with optional Cell Segmentation Staining User Guide (CG000760).

Post-instrument processing followed the Demonstrated Protocol Xenium In Situ Gene Expression - Post-Xenium Analyzer H&E Staining (CG000613).

Gene panels

The Xenium Human Multi-Tissue and Cancer Panel (377 genes) was pre-designed by 10x Genomics. The panel design was informed using single cell RNA sequencing data curated and reprocessed for standardization by the Human Protein Atlas. Genes were chosen to accurately type cells, and identify select immune, proliferation, and tumor markers, in human breast, lung, skin, liver, colon, kidney, lung cancer, and heart. The 100 custom genes were selected for identifying cells in human ovarian cancer.

The Xenium Prime 5K Human Pan Tissue and Pathways Panel was designed to enable comprehensive cell type and cell state identification using publicly available single cell RNA sequencing data. The panel also covers canonical signaling pathways, as well as genes relevant to developmental biology, immuno-oncology, and genes that are well known in biomedical literature.

Xenium Analyzer

The instrument run was performed following the Xenium Analyzer User Guide CG000584. The on-instrument analysis was run with Xenium Onboard Analysis v3.2.0. The data were reanalyzed with Xenium Ranger v4.0 using the xeniumranger resegment pipeline.

This dataset is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. 10x citation guidelines available here.