Mouse Brain Coronal Section 2 (FFPE)
Spatial Gene Expression dataset analyzed using Space Ranger 2.0.0
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10x Genomics obtained FFPE Mouse Brain tissue blocks from Avaden Biosciences. The tissue was sectioned as described in Visium CytAssist Spatial Gene Expression for FFPE – Tissue Preparation Guide Demonstrated Protocol (CG000518). Tissue sections of 5 µm was placed on a standard glass slide, then H&E-stained following deparaffinization. Sections were coverslipped with 85% glycerol, imaged, decoverslipped, followed by dehydration & decrosslinking Demonstrated Protocol (CG000520). The glass slide with tissue section was processed via Visium CytAssist instrument to transfer analytes to a Visium CytAssist Spatial Gene Expression slide. The probe extension and library construction steps follow the standard Visium for FFPE workflow outside of the instrument.
The H&E image was acquired using Olympus VS200 Slide Scanning Microscope with these settings:
- Olympus Objective magnification: 20x UPLXAPO Objective
- Numerical Aperture: 0.8
- ScopeLED light source: Xcite Novum
- Camera: VS-264C
- Exposure: 500 µs
Libraries were prepared following the Visium CytAssist Spatial Gene Expression Reagent Kits for FFPE User Guide (CG000495).
- Sequencing instrument: Illumina NovaSeq, flow cell HNNNMDSX3 (lane 1-2)
- Sequencing depth: 51,674 reads per spot
- Sequencing configuration: 28bp read 1 (16bp Visium spatial barcode, 12bp UMI), 90bp read 2 (transcript), 10bp i7 sample barcode and 10bp i5 sample barcode
- Dual-Index set: SI-TS-F1
- Slide: V42A20-353
- Area: D1
Key metrics were:
- Spots detected under tissue: 2,235
- Median genes per spot: 5,303
- Median UMI counts per spot: 14,491
This dataset is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. 10x citation guidelines available here.