Single-Cell Transcriptomic Profiling of the Tumor Microenvironment in Treatment-Naive Hepatocellular Carcinoma Patients
This study provides high-resolution single-cell RNA sequencing (scRNA-seq) data of tumor tissues from 12 treatment-naive hepatocellular carcinoma (HCC) patients. The dataset captures the transcriptomic profiles of diverse cell populations, including tumor cells, immune cells (e.g., T cells, B cells, macrophages), and stromal cells, revealing cellular heterogeneity and key gene expression signatures within the HCC tumor microenvironment (TME). This resource is critical for investigating HCC pathogenesis, identifying therapeutic targets, and developing immunotherapeutic strategies. Overall design: Samples: Fresh tumor tissues from 12 treatment-naive HCC patients with no prior surgery, chemotherapy, or radiotherapy,surgical puncture sample.  Single-cell preparation: Tissues were dissociated via mechanical disruption and enzymatic digestion, followed by fluorescence-activated cell sorting (FACS) or microfluidics to obtain high-quality single-cell suspensions.  Sequencing platform: Libraries were constructed using the 10x Genomics Chromium system and sequenced on Illumina NovaSeq 6000 (paired-end 150 bp).  Data analysis: Raw data processed via Cell Ranger pipeline for alignment and gene quantification; Seurat/R packages for cell clustering, annotation, and differential expression analysis. Cell subsets were annotated using canonical markers (e.g., EPCAM, CD3E, CD79A, CD68).  Quality control: Low-quality cells (genes <200 or mitochondrial gene ratio >20%) were excluded.