10x Genomics obtained FFPE mouse brain tissue from Adlego and embedded by BioIVT. The tissue was sectioned as described in Visium Spatial Gene Expression for FFPE – Tissue Preparation Guide Demonstrated Protocol (CG000408). Tissue sections of 5 µm were placed on Visium Gene Expression slides, then stained following Deparaffinization, H&E Staining, Imaging & Decrosslinking Demonstrated Protocol (CG000409).
- Sex: Male
- Age: >8 weeks
- Strain: C57BL/6
- Section Orientation: Coronal
The H&E image was acquired using Metafer Slide Scanning Microscope from MetaSystems with these settings:
- Zeiss Plan-Apochromat 20x objective
- Numerical Aperture: 0.8
- ScopeLED light source
- MetaSystems CoolCube 4c camera
Libraries were prepared following the Visium Spatial Gene Expression Reagent Kits for FFPE User Guide (CG000407 Rev A).
- Sequencing instrument: Illumina NovaSeq, flow cell HCYTVDSX2 (lane 1+2)
- Sequencing depth: 28,826 reads per spot
- Sequencing configuration: 28bp read 1 (16bp Visium spatial barcode, 12bp UMI), 120bp read2 (transcript), 10bp i7 sample barcode and 10bp i5 sample barcode
- Dual-Index set: SI-TS-B7
- Slide: V11J26-127
- Area: B1
Key metrics were:
- Spots detected under tissue: 2,264
- Median genes per spot: 6,160
- Median reads per spot: 28,826
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| Input Files | Size | md5sum |
|---|---|---|
| FASTQs | 4.36 GB | 0cb8adbfd42aa004d34c1f06f71f43da |
| Image (JPG) | 297 MB | 1a6642aa427d5105fe4fa2172533df28 |
| Probe Set | 2.31 MB | df6ad1d3e39c9406f5a728705d7aad3d |
| Output Files Format details | Size | md5sum |
|---|---|---|
| Genome-aligned BAM | 3.07 GB | 2e81ec1a653acf49386ac0e511e7d716 |
| Genome-aligned BAM index | 1.98 MB | ca4d5cfffb4ddb1efd62fb7f23f790c8 |
| Per-molecule read information | 197 MB | d7cd57374055c854a370636d2d4692fa |
| Feature / barcode matrix HDF5 (filtered) | 15.1 MB | 9bcc1d515feb13738578653e77acf8de |
| Feature / barcode matrix (filtered) | 45.9 MB | 017fc078b4aa21e1df39027d0bf3ccad |
| Feature / barcode matrix HDF5 (raw) | 27.1 MB | 510614bf875e6e6a5e5a397d82d05676 |
| Feature / barcode matrix (raw) | 72 MB | 2c3cf17a521c72d12807d956211f15ac |
| Clustering analysis | 24.3 MB | 0f931bc9701c2f851d93d284a2546b6d |
| Spatial imaging data | 10.6 MB | a78bb08009c4defd791354dd5c292bfa |
| Spatial Enrichment (Moran's I) | 1.81 MB | ebea327b145bf0cf2ab155c0cc30fdc1 |
| Summary CSV | 913 B | 4d41976279ed5c3c3bb1767c8103a918 |
| Summary HTML | 7.77 MB | 7093cdc056bc139e05954381c925e670 |
| Loupe Browser file | 2.56 GB | 0faed01097e7adb269452c6c356e21a8 |