10x Genomics obtained fresh frozen mouse brain tissue (Strain C57BL/6) from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols - Tissue Preparation Guide Demonstrated Protocol (CG000240). Tissue sections of 10 µm thickness from a sagittal slice of the anterior were placed on Visium Gene Expression Slides.
- Sex: Male
- Age: >8 weeks
- Strain: C57BL/6
- Section Orientation: Sagittal Slice of the Anterior
The H&E image acquired using a Nikon Ti2-E microscope with the following settings:
- Color camera
- 10X objective
- Numerical Aperture: 0.45
- Exposure: 10 ms
- Gain: 4.5X
The Visium Spatial Gene Expression library was prepared following the Visium Spatial Gene Expression Reagent Kits User Guide (CG000239). Sequencing data was processed using Space Ranger.
- Sequencing instrument: Illumina NovaSeq 6000
- Sequencing Depth: 129,730 read pairs per spot
- Sequencing Configuration: 28 x 120 bp
- Sequencing Coverage: Read 1 - 28 bp (includes 16 bp Spatial Barcode, 12 bp UMI); Read 2 - 120 bp (transcript); i7 sample index - 10 bp; i5 sample index - 10 bp.
- Dual-Index set T1T2-A4
- Slide: V19L29-035
- Area: D1
Key cell metrics were:
- Spots detected under tissue: 2,825
- Median UMI counts per spot: 20,145
- Median genes per spot: 5,338