GSM9521682: Sample 1 - Arc-Liver-A1; Homo sapiens; OTHER
Formalin-fixed paraffin-embedded (FFPE) human liver tissue blocks were sectioned at 5 µm thickness using a microtome. Sections were mounted onto positively charged glass slides according to 10x Genomics Visium HD sample preparation guidelines and stored at 4 °C with desiccant until further processing. Tissue sections were deparaffinized, stained with hematoxylin and eosin (H&E), and subjected to probe hybridization using the Visium Human Transcriptome Probe Set v2.1.0. Following hybridization and templated ligation, probe-derived products were transferred onto 10x Genomics Visium HD Spatial Gene Expression Slides (slide serial: H1-GVJMQ3Q) using the CytAssist instrument according to the manufacturer's protocol. Subsequent library preparation steps were performed following the Visium HD workflow. Spatial transcriptomic libraries were generated using the 10x Genomics Visium HD Spatial Gene Expression platform (SPATIAL-HD-v1 chemistry). Formalin-fixed paraffin-embedded (FFPE) human liver tissue sections were placed onto Visium HD capture areas (A1 and D1) of slide H1-GVJMQ3Q. Tissue sections were processed according to the manufacturer's instructions. Briefly, sections were deparaffinized, stained with hematoxylin and eosin (H&E), and imaged at 20× magnification using a Zeiss Axioscan 7 prior to probe hybridization. Imaging data were used for tissue detection and nucleus segmentation during downstream analysis. Gene expression profiling was performed using the Visium Human Transcriptome Probe Set v2.1.0 (GRCh38-2024-A reference). Probes were hybridized to target transcripts in situ and ligated using a templated ligation approach. Following probe ligation, captured molecules were released and subjected to library construction including amplification and indexing according to the Visium HD workflow. Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end 150 bp sequencing. During downstream processing, read 2 was trimmed to 50 bp in Space Ranger Count v4.0.1. Raw sequencing data were processed using Space Ranger Count v4.0.1 with probe filtering enabled, intronic reads excluded, UMI registration applied, and nucleus segmentation performed during image processing.