Preview Data: FFPE Human Skin Primary Dermal Melanoma with 5K Human Pan Tissue and Pathways Panel

Overview

Xenium Prime 5K In Situ Gene Expression with Cell Segmentation Staining data for human skin melanoma tissue (FFPE) using the Xenium Prime 5K Human Pan Tissue and Pathways Panel.

This sample represents a Primary Dermal Melanoma of the skin, featuring necrosis along the outer edge of the dermis and cancerous cells. Hematoxylin and eosin (H&E) staining reveals abundant tumor cells within the dermis, with evidence of pyknosis (darkly stained, shrunken nuclei) indicating cell death.

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

FFPE-preserved tissue was purchased from Discovery Life Sciences (Skin - Right Lower Extremity, Melanoma).

Tissue preparation

Tissues were prepared following the Demonstrated Protocols Xenium In Situ for FFPE - Tissue Preparation Guide (CG000578) and Xenium In Situ for FFPE Tissues – Deparaffinization & Decrosslinking (CG000580).

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 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.

A development version of the Xenium Human 5K Pan Tissue and Pathways Panel that targets 5,006 genes was used to generate this dataset. The following genes were removed from the final 5K panel due to their subpar performance (non-specific binding): ADGRG1, NMBR, OSMR, OSTF1, and RGS8.

Xenium Analyzer

The instrument run was performed following the Xenium Analyzer User Guide CG000584. The on-instrument analysis was run with Xenium Onboard Analysis v3.0.0.

This dataset is licensed under the Creative Commons Attribution license.