GSM6415705: Tumour 1 (T1); Homo sapiens; RNA-Seq
Spatial transcriptomics was performed on Formalin Fixed Paraffin Embedded (FFPE) tissue sections using the 10X Genomics Visium Spatial Gene Expression platform (10X Genomics, Pleasanton, CA, USA). Using a Leica RM2235 microtome (Leica, Germany), 5 µm tissue sections were cut from FFPE tissue blocks and placed within the etched frames of the capture areas on the active surface of the Visium Spatial Slide. Slide was dried in an oven overnight at 37°C then at 60°C during 25 minutes before dehydration in ethanol and Hematoxylin & Eosin (H&E) staining. Slide was finally transferred to water and mounted in 87% glycerol before image acquisition the same day. Image mosaic of each section was acquired at 5X and 20X magnification (Zeiss EC Plan-Neofluar 5x/0.16, Zeiss Plan-Apochromat 20x/0.8) with transmitted white light and a Zeiss colour camera Zeiss Axiocam Color on a Zeiss Axio Observer microscope to generate a brightfield image of each section including the fiducial markers frame. The final stitched mosaic was created with Zeiss ZEN Stitching module. Stained FFPE tissue sections were strictly processed as outlined in the demonstrated protocol « Visium Spatial Gene Expression Reagent kits for FFPE, UserGuide » (Part number CG000407, RevC). Quantification and quality control of the final libraries were performed using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).