Fresh Frozen Mouse Brain Replicates
In Situ Gene Expression dataset analyzed using Xenium Onboard Analysis 1.0.2
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Demonstration of gene expression profiling for fresh frozen mouse brain on the Xenium platform using the pre-designed Mouse Brain Gene Expression Panel (v1). Replicate results demonstrate the high reproducibility of data generated by the platform.
10x Genomics obtained tissue from a C57BL/6 mouse from Charles River Laboratories. Three adjacent 10µm sections were placed on the same slide. Tissues were 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 Replicate tabs. 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 | Replicate 1 | Replicate 2 | Replicate 3 |
|---|---|---|---|
| Median transcripts per cell | 252 | 250 | 253 |
| Cells detected | 162,033 | 154,654 | 158,047 |
| Decoded transcripts per 100 µm² | 107.0 | 102.1 | 105.6 |
| Total transcripts detected | 49,587,802 | 47,093,471 | 48,460,389 |
| Scanned tissue area (cm²) | 0.63 | 0.64 | 0.61 |
This dataset is licensed under the Creative Commons Attribution license.