Mouse Brain Section (Coronal)
Spatial Gene Expression dataset analyzed using Space Ranger 1.1.0
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10x Genomics obtained fresh frozen mouse brain tissue 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 slice of the coronal plane were placed on Visium Gene Expression slides, then stained following the Methanol Fixation, H&E Staining & Imaging Demonstrated Protocol (CG000160).
- Sex: Male
- Age: >8 weeks
- Strain: C57BL/6
- Section Orientation: Coronal
The slide was coverslipped and the H&E image acquired using a Nikon Ti2-E microscope with the following settings:
- Color camera
- 10X objective
- Numerical Aperture: 0.45
- Exposure: 2 ms
- Gain: 4.5X
The Visium Spatial Gene Expression libraries were prepared following the Visium Spatial Gene Expression Reagent Kits User Guide (CG000239 Rev A).
- Sequencing instrument: Illumina NovaSeq 6000
- Sequencing depth: 115,569 reads per spot
- Sequencing configuration: Paired-end (28 X 90), Dual-Indexed Sequencing. Read 1: 28bp read 1 (16bp Visium spatial barcode, 12bp UMI), Read 2: 120bp (transcript), 10bp i7 sample barcode and 10bp i5 sample barcode
- Dual-index set T1T2-E3
- Slide: V19L01-041
- Area: C1
Key cell metrics were:
- Spots detected under tissue - 2,702
- Median UMI counts per spot - 28,944
- Median genes per spot - 6,018
This dataset is licensed under the Creative Commons Attribution license.