Normal Human Prostate (FFPE)
Spatial Gene Expression dataset analyzed using Space Ranger 1.3.0
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10x Genomics obtained FFPE human prostate tissue from Indivumed Human Tissue Specimens. 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 1E333_Tn17
- Sex: Male
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 HLM27BGXF (lane 1-4)
- Sequencing depth: 28,464 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-D2
- Slide: V11J26-011
- Area: D1
Key metrics were:
- Spots detected under tissue: 2,543
- Median genes per spot: 2,945
- Median UMI counts per spot: 5,467
This dataset is licensed under the Creative Commons Attribution license.