GSM9452692: Patient 43-pre biopsy Visium; Homo sapiens; OTHER
Tumor samples (FFPE) with adequate cellularity underwent spatial transcriptomics using the Spatial Gene Expression Slide & Reagent kit (10x Genomics). Tissue permeabilization was performed for 12-18 minutes for each sample, which was determined by the tissue optimization assay, and sequencing libraries were generated following standard protocols by Abiosciences. Samples were prepared by embedding in OCT and sectioning, then placing one 10um section of frozen tissues onto one 6.5 mm x 6.5 mm capture area of the 10x Genomics Visium spatial gene expression slide (v1), fixed, stained with H&E, imaged, followed by permeabilization, reverse transcription and spatial barcoding followed by denaturing to release the cDNA, and library construction. For 10x Visium Spatial transcriptome library preparation, we followed the 10x user guides (G000238: Visium Spatial Tissue Optimization User Guide and CG000239: Visium Spatial Gene Expression Reagent Kits User Guide).  The libraries are then sequenced in an Illumina sequencer NovaSeq6000 with the specifications based on 10x Genomics user guide to obtain at least 50,000 read pairs per tissue-covered spot.