GSM9556001: Patient 032, pre-treatment; Homo sapiens; OTHER
FFPE 5µm tissue sections were deparaffinized, H&E stained and imaged. The tissue was permeabilized and 10x Genomics Human Transcriptome V2 probes were hybridized to the mRNA overnight. Probes were ligated before being placed in the 10x Genomics CytAssist instrument for probe release and capture by spatially barcoded spots on a Visium CytAssist HD Gene Expression slide. Sequencing libraries were prepared following the 10x Genomics Visium HD Spatial Gene Expression Reagent Kits User Guide. Briefly, captured probes were subjected to extension and denaturation from slide, followed by real-time PCR quantification to determine optimal sample index PCR cycles to complete the Illumina-ready library. Final library quality was assessed using the LabChip GXII HT (PerkinElmer) and libraries were quantified by Qubit (ThermoFisher). Pooled libraries were subjected to 151bp paired-end sequencing according to the manufacturer's protocol (Illumina NovaSeqX Plus for all samples except 013 samples, which were sequenced on an Illumina NovaSeq 6000).