GSM9554205: Spatial transcriptomics (Visium) of Human Colorectal Cancer Capture 2 (CRC_BIC18_2); Homo sapiens; OTHER
Prior to processing Visium gene expression samples, DV200 was measured on RNA isolated from Formalin-fixed paraffin-embedded (FFPE) blocks to assess RNA integrity. Samples with a DV200 greater than 50% were selected for subsequent steps. After quality control, blocks were trimmed and 5-µm tissue sections were cut and placed on the capture area of a Visium Spatial Gene Expression for FFPE slide (10X Genomics). The slide was incubated in a thermal cycler at 42 °C for 3 h, and then placed in a desiccator overnight at room temperature. Subsequent steps covering tissue staining and library preparation were performed according to the manufacturer's instructions (CG000407_VisiumSpatialGeneExpressionforFFPE_RevC). The quality of the libraries was assessed using an Agilent 4200 TapeStation. Libraries were sequenced using the NovaSeq 6000 platform with 150 paired-end configuration on a NovaSeq SP flowcell.