Fresh Frozen Mouse Brain for Xenium Explorer Demo
In Situ Gene Expression dataset analyzed using Xenium Onboard Analysis 1.0.2
Learn about Xenium analysis
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
| Metric | Full coronal section | Tiny subset |
|---|---|---|
| Median transcripts per cell | 218 | 211 |
| Cells detected | 130,870 | 36,602 |
| Decoded transcripts per 100 µm² | 75.1 | 79.9 |
| Total transcripts detected | 34,367,436 | n/a |
| Scanned tissue area (cm²) | 0.66 | n/a |
This dataset is licensed under the Creative Commons Attribution license.