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Mouse Brain Serial Section 1 (Sagittal-Posterior)

Spatial Gene Expression dataset analyzed using Space Ranger 1.0.0

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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 posterior were placed on Visium Gene Expression Slides.

  • Sex: Male
  • Age: >8 weeks
  • Strain: C57BL/6
  • Section Orientation: Sagittal Slice of the Posterior

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: 87,180 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-F3
  • Slide: V19L29-035
  • Area: A1

Key cell metrics were:

  • Spots detected under tissue - 3,353
  • Median UMI counts per spot - 14,864
  • Median genes per spot - 4,564

This dataset is licensed under the Creative Commons Attribution license.