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Adult Mouse Brain Coronal Section (Fresh Frozen)

Spatial Gene Expression dataset analyzed using Space Ranger 2.1.0

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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 and imaged following the Methanol Fixation, H&E Staining & Imaging Demonstrated Protocol (CG000160).

The slide was cover-slipped 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

Visium Spatial Gene Expression Library

Libraries were prepared following the Visium Spatial Gene Expression Reagent Kits User Guide (CG000239 Rev F).

  • Sequencing instrument: Illumina NovaSeq
  • Sequencing configuration: Paired-end (28 X 90)
  • Sequencing coverage: 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: SI-TT-E4
  • Slide: V10L08-332
  • Area: C1

This dataset is licensed under the Creative Commons Attribution license.