GSM7500358: DMBA/TPA-induced skin tumor Visium Spatial Transcriptomics, replicate 1 (A1_230331); Mus musculus; OTHER
A microarray of fresh-frozen DMBA/TPA-induced squamous cell carcinoma samples, surgically removed from mouse back skin, was cryo-sectioned with a 10µm thickness (Leica, CM3050S) and placed on the capture area of a spatial gene expression slide (10x Genomics, 1000188), resulting in 4 different tumors on a single capture area. Samples were stored in -80°C before processing. The workflow of Mirzazadeh et al. (2023) for RNA-Rescue Spatial Transcriptomics (RRST) was followed to overcome low RNA integrity number (RIN) score. The samples were fixed with 4% PFA and hematoxylin and eosin (H&E) staining was performed. The spatial libraries were then generated from the probe hybridization step (10x Genomics, 1000365) according to Visium Spatial Gene Expression Reagent Kits for FFPE (10x Genomics, User Guide CG000407 Rev D, 1000361). The resulting libraries were sequenced by the Genomics Facility Basel. The sequencing was performed in a paired-end manner with dual indexing (10x Genomics, 1000251) on a NovaSeq 6000 (Illumina) with a S4 flow cell. Libraries were then sequenced with the following cycle settings: Read1 101 cycles, i7 10 cycles, i5 10 cycles, Read2 101 cycles.