title: Spatial Transcriptome of Mus musculus: adult brain
design: Animals were euthanized, and brains were dissected for snap-freezing in a mixture of chilled isopentane and dry ice. The tissues were then embedded in Tissue Tek OCT compound. Subsequently, tissue blocks were sectioned into 10-micron thick slices and mounted on barcoded 10x Genomics Visium slides.The tissue sections were optimized according to the 10x Genomics protocol CG000238-RevE. Briefly, the sections were fixed in methanol, followed by immunostaining, and then scanned using an EVOS M7000 microscope with a 10x objective lens. As per manufacturer protocol CG000239-RevF: samples underwent permeabilization, reverse transcription, second strand synthesis, denaturation, and cDNA synthesis. Quality control was performed using an Agilent 2100 Bioanalyzer with High Sensitivity DNA chips. The samples were then enzymatically fragmented, and double size selection was performed using SPRIselect reagent. Unique indexes and primers were added to the libraries using the Dual Index Kit TT Set A (PN-1000215). Finally, the libraries were sequenced on an Illumina NovaSeq 6000 platform using paired-end sequencing (PE150) through NovogeneAIT Genomics, Singapore Pte Ltd.