Datasets

Fresh Frozen Mouse Brain for Xenium Explorer Demo

In Situ Gene Expression Dataset by Xenium Onboard Analysis 1.0.2

To try a demo of Xenium Explorer in your browser, check out our fresh frozen mouse brain demo.Click here
  • Files

Inputs/Slide

Demonstration of gene expression profiling for fresh frozen mouse brain on the Xenium platform using the pre-designed Mouse Brain Gene Expression Panel (v1).

10x Genomics obtained a 10µm section from a C57BL/6 mouse from Charles River Laboratories. The tissue was prepared following the demonstrated protocols Xenium In Situ for Fresh Frozen Tissues - Tissue Preparation Guide (CG000579) and Xenium In Situ for Fresh Frozen Tissues – Fixation & Permeabilization (CG000581).

How to view data

Shared files are displayed in the Inputs/Slide tab and per-sample output files are in the Full coronal section and Tiny subset tabs. The subset dataset includes the cortex and hippocampus of one hemisphere from the full coronal section. The subset dataset's smaller file size makes running analysis tutorials and Xenium Explorer demos faster. Interactively explore data with Xenium Explorer by downloading the Xenium Output Bundle file. Load the Gene Groups CSV to create gene groups based on cell type markers.

Key metrics

MetricFull coronal sectionTiny subset
Median transcripts per cell218211
Cells detected130,87036,602
Decoded transcripts per 100 µm²75.179.9
Total transcripts detected34,367,436n/a
Scanned tissue area (cm²)0.66n/a

Published on January 22nd, 2023

This dataset is licensed under the Creative Commons Attribution license.

Files Download

Downloading is unavailable on mobile devices.
If the file size is large, we suggest using instead.
Input FilesSizemd5sum
Panel (JSON)129 kBb6a76e15cd12f5e79757a98766483bbe
Supplemental: Gene Groups (CSV)4.34 kB8c1917c58b913e4ba1d4421aeabcd574