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Adult Mouse Brain (FFPE)

Spatial Gene Expression dataset analyzed using Space Ranger 1.3.0

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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

This dataset is licensed under the Creative Commons Attribution license.