Adult Mouse Kidney (FFPE)
Spatial Gene Expression dataset analyzed using Space Ranger 1.3.0
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Dataset overview
Output and supplemental files
Input files
Learn about Visium analysis
10x Genomics obtained FFPE mouse kidney 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: Sagittal
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 H2LN2DMXY (lane 1-2)
- Sequencing depth: 53,993 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-G6
- Slide: V11A13-021
- Area: C1
Key metrics were:
- Spots detected under tissue: 3,124
- Median genes per spot: 7,260
- Median UMI Counts per spot: 32,310
This dataset is licensed under the Creative Commons Attribution license.