GSM9128541: Pten/Trp53; Mus musculus; OTHER
Tissue section was cut at 5 µm from a FFPE tissue block using a Leica RM2165 microtome (Leica) and placed on a Superfrost Plus Epredia™ slide (Thermo Fisher Scientific). The tissue slide was dried for 3 hours at 42°C followed by overnight storage in a slide mailer containing a desiccant at room temperature (Demonstrated protocol CG000518 Rev. B, 10X Genomics). Subsequently, the section was deparaffinized and stained for hematoxylin and eosin (H&E) according to 10X Genomics recommendation (Demonstated protocol CG000520 Rev. A) before imaging at 20X magnification using a Hamamatsu NanoZoomer 2.0HT digital slide scanner in raw data mode, generating a TIFF file. Stained sections were then decrosslinked and strictly processed as outlined in the demonstrated protocol « Visium CytAssist Spatial Gene Expression Reagent kits for FFPE, UserGuide » (Part number CG000495, Rev. C, 10X Genomics). Briefly, A mouse whole transcriptome probe panel (Mouse Visium transcriptome probes v1), with one specific probe pair per targeted gene, was hybridized and ligated to the tissue, after which gene expression probes were released and captured by spatially barcoded oligonucleotides on the Visium CytAssist Spatial Gene Expression v2 slide, 6.5 mm using the CytAssist instrument. The captured probes were then used to prepare a gene expression library for sequencing, with spatial barcodes enabling the mapping of reads back to their original tissue locations. Quantification and quality control of the final library were performed using Bioanalyzer 2100 (Agilent Technologies).