title: Spatial transcriptomics of seven hepatocellular carcinoma cases
design: Spatial transcriptomics of seven hepatocellular carcinoma cases
library_construction_protocol: HCC samples, including the tumor-non-tumor boundary, were collected from seven patients who underwent hepatic resection at the Department of Surgery, Kyoto University Hospital. Tissue specimens, approximately 10 × 10 mm in size, were excised from the tumor-non-tumor boundary immediately after hepatic resection. The samples were fixed in 10% neutral buffered formalin for 6–48 h. Fixed samples were embedded in formalin-fixed paraffin-embedded (FFPE) blocks and stored under refrigeration until sectioning. 5 µm sections were prepared and processed according to the 10x Genomics Visium CytAssist Spatial Gene Expression for FFPE protocol (CG000520, Rev B). This protocol included deparaffinization, hematoxylin and eosin staining, imaging, and decrosslinking steps. High-resolution histological images were captured with an APX100 microscope (Evident).  Library preparation was subsequently performed according to the Visium CytAssist Spatial Gene Expression Reagent Kit (CG000495, Rev B) for human transcriptomes on slides with 6.5 mm or 11 mm capture areas.