ArticleMolecular medicine reports2022
Comparison of single‑nucleus and single‑cell transcriptomes in hepatocellular carcinoma tissue.
Article in Molecular medicine reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed, 49 citations in OpenAlex.
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- Single-Cell Transcriptomic Profiling Reveals Immunometabolic Reprogramming and Cell-Cell Communication in the Tumor Microenvironment of Human Hepatocellular Carcinoma.International journal of molecular sciences · 2026Article
- Integrative machine learning and multi-omics analysis reveals ATIC as a promoter of hepatocellular carcinoma progression.Scientific reports · 2026Article
- Reduction in Hepatic Phosphatidylcholine Biosynthesis Promotes MASH Through Copper Deficiency.bioRxiv : the preprint server for biology · 2026Article
- New biological insights into osteosarcoma-lessons from single cell sequencing studies.Cancer metastasis reviews · 2026Review
- Hematopoietic Cell Kinase Promotes Cerebral Ischemic Injury and Mitochondrial Dysfunction via p38 Activation in Ischemic Stroke.Molecular neurobiology · 2026Article
- The tumor-associated fibroblasts regulate urothelial carcinoma progression.Journal of molecular cell biology · 2026Article
- Leveraging Single-Cell Technologies to Advance Understanding of Myocardial Disease.Circulation research · 2026Review
- Comparative Single-Cell Transcriptomics Uncovers Shared and Distinct Molecular Signatures in Cystic Fibrosis and Primary Ciliary Dyskinesia.bioRxiv : the preprint server for biology · 2025Article
- Single cell transcriptional analysis of human adenoids identifies molecular features of airway microfold cells.Mucosal immunology · 2025Article
- Establishing single cell RNA transcriptomics: a brief guide.Frontiers in zoology · 2025Review
- Metabolism archetype cancer cells induce protumor TREM2Nature communications · 2025Article
- Role of progesterone action in inguinal hernia formation via skeletal muscle fibrosis and atrophy.JCI insight · 2025Article
- Approaching the holistic transcriptome-convolution and deconvolution in transcriptomics.Briefings in bioinformatics · 2025Review
- Single nuclear-spatial transcriptomic sequencing reveals distinct puncture-induced cell subpopulations in the intervertebral disc of a rat model.Clinical and translational medicine · 2025Article
- Single-Cell RNA Sequencing Outperforms Single-Nucleus RNA Sequencing in Analyzing Pancreatic Cell Diversity and Gene Expression in Goats.International journal of molecular sciences · 2025Article
- Missing cell types in single-cell references impact deconvolution of bulk data but are detectable.Genome biology · 2025Article
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Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single‑nucleus RNA sequencing (snRNA‑seq) is a method used to analyze gene expression in cells for which isolation is complex, such as those in hepatocellular carcinoma (HCC) tissues. It constitutes an alternative to single‑cell RNA sequencing (scRNA‑seq) by analyzing the nucleus rather than the whole cell; however, whether it can completely replace scRNA‑seq in HCC remains to be clarified. In the present study, scRNA‑seq was compared with snRNA‑seq in tumor tissue obtained from patients with HCC, using the 10X Genomics Chromium platform. Seurat was also used to process the data and compare the differences between the two sequencing methods in identifying different cell types. In the present study, the transcriptomes of 14,349 single nuclei and 9,504 single cells were obtained from the aforementioned HCC tissue. A total of 21 discrete cell clusters, including hepatocytes, endothelial cells, fibroblasts, B cells, T cells, natural killer cells and macrophages were identified. Notably, a high number of hepatocytes were detected using snRNA‑seq, while an increased number of immunocytes were identified in the tumor microenvironment using scRNA‑seq. Results of the present study provided a comprehensive image of human HCC at a single‑cell resolution. Moreover, results of the present study further demonstrated that snRNA‑seq may be adequate in replacing scRNA‑seq in certain cases, and snRNA‑seq performs at an improved level in hepatocyte sequencing. Combined use of the two sequencing methods may contribute to the study of intercellular interactions.
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