Xenium Human Brain Preview Data

In Situ Gene Expression dataset analyzed using Xenium Onboard Analysis 1.3.0

This preview dataset was generated using a preliminary version of the human brain gene panel and may be replaced with data generated using the final panel in the future.

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Dataset overview

Output and supplemental files

Input files

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Overview

Preview of Xenium In Situ Gene Expression data for adult human brain cortical sections, using a development version of the Human Brain Gene Expression Panel and two custom add-on panels for brain cell types.

Biomaterials

Three brain sections were used:

Adult human brain cortical section, healthy (from Acepix Biosciences)
Adult human brain with glioblastoma multiforme (from Avaden Biosciences)
Adult human brain with Alzheimer’s (from Acepix Biosciences)

Tissue preparation

The first two sections (healthy and glioblastoma) were placed on the same slide and the third section (Alzheimer's) was placed on a second slide. 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).

Gene panels

The Xenium Human Brain Gene Expression Panel was pre-designed by 10x Genomics to identify cells in healthy, cancer, and neurodegenerative brains, including neuronal, endothelial, astrocytes, microglia, oligodendrocytes, immune cell types, and tumor cells. The base panel was used for all three sections.

Two add-on panels were used in addition to the base panel. On the first slide, with the healthy and glioblastoma samples, an add-on panel of 65 genes was used to increase resolution of cell types found in healthy human brains. On the second slide, with the Alzheimer's sample, an add-on panel of 100 genes specific to Alzheimer's disease selected from the literature was used. Base panels were combined with add-on panels into a single JSON file for each run, and uploaded to the Xenium Analyzer instrument using a USB.

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 1.3.0.

Metric	Healthy	Glioblastoma	Alzheimer's
Median transcripts per cell	166	216	216
Cells detected	24,406	40,887	44,955
Decoded transcripts per 100 µm²	41.9	65.5	59.8
High quality transcripts detected	6,011,583	13,324,742	14,006,920
Scanned tissue area (cm²)	0.35	0.37	0.43

How to view data

Select a tab at the top of the page to view outputs for each section. Interactively explore data with Xenium Explorer by downloading the Xenium Output Bundle file. See the Getting Started with Xenium Explorer page for more details.

This dataset is licensed under the Creative Commons Attribution license.