Human Kidney Preview Data (Xenium Human Multi-Tissue and Cancer Panel)

In Situ Gene Expression dataset analyzed using Xenium Onboard Analysis 1.5.0

This preview dataset was generated using a preliminary version of the Xenium Human Multi-Tissue and Cancer Panel and may be replaced with data generated using the final panel in the future.

Assess data quality

View summary metrics to assess data quality and more.

Visualize and explore data

Discover differentially expressed genes, visualize your favorite genes, and explore your data with our visualization software.

Dataset overview

Output and supplemental files

Input files

Learn about Xenium analysis

Overview

Preview of Xenium In Situ Gene Expression data for adult human kidney sections, using a development version of the Xenium Human Multi-Tissue and Cancer Panel.

Biomaterials

Two FFPE tissue microstrips, including multiple tissue samples within a single FFPE donor block, were purchased from AcePix Biosciences. The first tissue block represents a non-diseased kidney section, while the second block was diagnosed with kidney cancer (papillary renal cell carcinoma, or PRCC).

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).

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, lymph node, and heart.

Xenium Analyzer

The instrument run was performed following the Xenium Analyzer User Guide CG000584. The on-instrument analysis was run with Xenium Onboard Analysis version 1.5.0.

Metric	Non-diseased	Cancer (PRCC)
Median transcripts per cell	54	57
Cells detected	97,560	56,510
Decoded transcripts per 100 µm²	38.3	36.3
High quality transcripts detected	6,721,196	4,052,443
Region area (µm²)	24,106,589	17,102,908

How to view data

Interactively explore data with Xenium Explorer by downloading the Xenium Output Bundle file. 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.

This dataset is licensed under the Creative Commons Attribution license.