10x Genomics obtained FFPE human breast tissue from BioIVT Asterand Human Tissue Specimens. The tissue was annotated with Ductal Carcinoma In Situ, Invasive Carcinoma. 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).
- Block 738811QB Section 1. Grade II
- Sex: Female
- Ethnicity: Asian
- Age: 73
Annotations here were done at an overview level and were performed by Agoko NV, Belgium.
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 H25NJDMXY (lane 1)
- Sequencing depth: 32,524 reads per spot
- Sequencing configuration: 28bp read 1 (16bp Visium spatial barcode, 12bp UMI), 50bp read2 (transcript), 10bp i7 sample barcode and 10bp i5 sample barcode
- Dual-Index set SI-TS-B12
- Slide: V11J26-008
- Area: B1
Key metrics were:
- Spots detected under tissue: 2,518
- Median genes per spot: 5,244
- Median reads per spot: 32,524
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| Input Files | Size | md5sum |
|---|---|---|
| FASTQs | 5.28 GB | a0a33519d17367a4488f946d412e2f73 |
| Image (TIFF) | 103 MB | eed639b786b5226b4b1cc97e40fd1a5c |
| Probe Set | 2.08 MB | 39ecfeb3651c14d45900d843d6502525 |
| Output Files Format details | Size | md5sum |
|---|---|---|
| Genome-aligned BAM | 3.83 GB | 2ccff0b9abbb03ef659bc28f7f8c6445 |
| Genome-aligned BAM index | 2.27 MB | 5325ca6d950b20fac45054d8ccf93fe2 |
| Per-molecule read information | 181 MB | 974625c1db2eb641b57c092c3d2bb875 |
| Feature / barcode matrix HDF5 (filtered) | 14 MB | 51bc85964122c30244405e2331727ff6 |
| Feature / barcode matrix (filtered) | 41.5 MB | 327eb8eca13ab31dde38a253d4a7678d |
| Feature / barcode matrix HDF5 (raw) | 22.7 MB | fc1841321cc9eba7129fe3684c765cdb |
| Feature / barcode matrix (raw) | 58.3 MB | 850bc480b68367bd65e9483f85d6e24b |
| Clustering analysis | 25.9 MB | 1807707b61224f67f6a0c2b946526a58 |
| Spatial imaging data | 8.32 MB | 9a6bc80f4c1e288db5e9bcd368d473c3 |
| Spatial Enrichment (Moran's I) | 1.85 MB | 8e7653cd85fc745481fd13781426cfcb |
| Summary CSV | 913 B | 3e9a3cef59eb7431d7651401594c0b7c |
| Summary HTML | 7.39 MB | ab01b15b4694504b45c82ac0feb36776 |
| Loupe Browser file | 1.02 GB | ad5aa7b2e9e4deb6b81158120eb61a5a |