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.
The H&E images of each section were acquired using a Nikon Ti2-E microscope with the following settings:
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.
For individual section level metrics, refer to the dataset pages:
Key metrics were: