Aggregate of Mouse Brain Sections: Visium Fresh Frozen, Whole Transcriptome

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). Serial tissue sections of 10 µm thickness from a sagittal slice of the anterior and posterior regions were placed on the same Visium Gene Expression Slide.

• Sex: Male
• Age: >8 weeks
• Strain: C57BL/6

The H&E images of each section were 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

Visium Spatial Gene Expression Library

Individual libraries for each section were prepared following the Visium Spatial Gene Expression Reagent Kits User Guide (CG000239). Sequencing data of the individual sections was first processed using spaceranger count. The outputs were then aggregated and normalized to equal sequencing depth using the spaceranger aggr pipeline to generate a single set of output files containing all of the data from each of the individual samples.

• Sequencing instrument: Illumina NovaSeq 6000
• 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.
• Slide: V19L29-035

For individual section level metrics, refer to the dataset pages:

• Mouse Brain Section 2 (Sagittal-Anterior)
• Mouse Brain Section 2 (Sagittal-Posterior)

Key metrics were:

• Spots detected under tissue - 6,112
• Median UMI counts per spot - 15,550
• Median genes per spot - 4,715

This dataset is licensed under the Creative Commons Attribution license.