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 UMI Counts per spot: 17,614