biostudies-arrayexpressTAKAHIRO NISHIOHomo sapiensSpaceRangerhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-1522610x Genomics Visium v2 spatial transcriptomic analysis of seven hepatocellular carcinoma (HCC) cases. The patients’ underlying liver diseases were metabolic-associated steatohepatitis (MASH, n = 2), hepatitis C (n = 2), hepatitis B (n = 1), and alcoholic liver disease (n = 1).biostudies-arrayexpressSequencing - Libraries were sequenced on the NovaSeq X Plus (Illumina) in a 150 × 150 bp paired-end configuration.Library Construction - 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.Sample Collection - 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.Nucleic Acid Extraction - 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).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Reads were aligned to the GRCh38 human reference genome using the Space Ranger v3.0 (10x Genomics).UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq Xspatial transcriptomics by high-throughput sequencingHomo sapiensTAKAHIRO NISHIOYO OGUMAfalseSpatial transcriptomics of seven hepatocellular carcinoma cases10x Genomics Visium v2 spatial transcriptomic analysis of seven hepatocellular carcinoma (HCC) cases. The patients’ underlying liver diseases were metabolic-associated steatohepatitis (MASH, n = 2), hepatitis C (n = 2), hepatitis B (n = 1), and alcoholic liver disease (n = 1).2025-12-31T00:00:00Z2025-12-31T02:02:47.567Z2025-06-13T11:15:58.992ZE-MTAB-15226ERP173446EFO_0002944EFO_0004170EFO_0030005EFO_0005518EFO_0003816EFO_0004184