title: GSM8863903: Lung, SNL LUSC GEMM, 11Months post Ad-Cre; Mus musculus; OTHER
library_name: GSM8863903
library_construction_protocol: Mice were euthanized by intraperitoneal administration of an overdose of Avertin at the indicated time-points. Lungs were inflated and perfused through the trachea with 4% paraformaldehyde (PFA), fixed overnight, washed in 1xPBS for 24-48h, then transferred to 70% ethanol and subsequently embedded in paraffin. Sections were cut and stained with H&E by the UTSW HistoPathology Core. The H&E slides were scanned at 40x magnification using the Leica Biosystems Aperio AT2 DX brightfield slide scanner. Regions of lung adenocarcinoma and lung squamous cell carcinoma morphology were annotated. The regions of interest for spatial transcriptomics were digitally annotated using QuPath (v.5.0.1) and exported as a TIFF image file. Tissue slides were decoverslipped, washed, and rehydrated following the 10x Genomics Visium CyAssist Tissue Preparation Guide (CG000518 rev. B). Slides were immersed in xylene then placed on a metal block cooled with dry and the coverslip was removed with a razor blade. Sections were washed and rehydrated by sequential immersions in xylene, 100% ethanol, 96% ethanol, and 70% ethanol, according to manufacturer recommendations. A region of the tissue outside of the region of interest was cut away for RNA quality control. RNA was isolated with the Qiagen RNeasy Mini Kit (cat: 74104), and quality was evaluated using the Agilent Technologies RNA 6000 Pico kit (cat: 5067-1513) with a DV200 assay in the Agilent 2100 BioAnalyzer. Spatial transcriptomics libraries were prepared with the following the 10x Genomics Visium CyAssist Tissue Preparation kit and protocol according to manufacturer's guidelines.
identifiers.namespace: GEO
identifiers.id: GSM8863903_r1