GSM8727282: ST1; Homo sapiens; OTHER
Slides for 10X Visium were freshly cut (10uM) from Formalin fixed paraffin embeded GBM tissues, after determining RNA quality. 10X-Visium was used to perform spatial transcriptomics (ST) on two GBM specimens, with distinct genetic background and patient sex, in which highest RNA quality was obtained and full Core-to-Margin transition was captured histologically. Tissue permeabilization and library preparation was done according to the manufacturer's protocol. The Visium spatial gene expression for FFPE assays (10X Genomics) was used to generates spatially-resolved cDNA libraries from FFPE tissue. Tissue slices were sectioned onto the assay slide, which consists of four 6.5mm x 6.5mm arrays of spatially-barcoded poly T capture probes (arranged as 5,000 55 um spots) and permeabilized. Captured mRNA then underwent reverse transcription and cleavage from the slide, followed by cDNA amplification and fragmenting, end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing following the manufacturer's protocol. Libraries were quantified using Tapestation and Qubit and sequenced in paired end mode on NovaSeq instrument targeting a depth of 50,000-100,000 reads per capture spot.