GSM7853984: STAD-G2; Homo sapiens; OTHER
ST on FFPE slides were performed with the Visium spatial technology from 10X Genomics. Two to three consecutive tissue sections of 5-μm thickness were collected for RNA extraction with the Qiagen RNeasy FFPE Kit. To assess the RNA quality of the tissue, the purified RNA was immediately processed to calculate the percentage of total RNA fragments >200 nucleotides (DV200) using the Agilent RNA 6000 Pico Kit. Based on DV200 evaluation, blocks with DV200 >30% were selected for proceeding with sectioning. The area of interest (11 x 11 mm) on section was carefully placed within the allowable area to ensure compatibility with the Visium CytAssist instrument. The tissues were then deparaffinized, stained, and decross-linked, followed by probe hybridization, ligation, CytAssist enabled RNA digestion and oligo capture, release, and extension. The Visium spatial gene expression FFPE libraries were constructed using the Visium CytAssist Spatial Gene Expression for FFPE Human Transcriptome Probe Kit (PN-1000444) following the manufacturer's guidance. Constructed libraries were sequenced on the Illumina NovaSeq 6000 platforms to achieve a depth of at least 75,000 mean read pairs per spot.