ArticleBMC genomics2014
RNA-Seq gene expression profiling of HepG2 cells: the influence of experimental factors and comparison with liver tissue.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 50 citations in OpenAlex.
- Evaluation of the Immortalized Primary Human Hepatocyte Cell Line Fa2N-4 as a Model for Metabolic Dysfunction-Associated Steatotic Liver Disease.Gastro hep advances · 2026Article
- Calcitriol Induces Paraoxonase 1 Expression in HepG2 Cells: Possible Involvement of VDR-Dependent and Alternative Pathways.International journal of molecular sciences · 2025Article
- Comparative Proteomic Characterization of Serum-Free Cultivated HepG2 Cells Reveals Upregulated Drug Metabolism and Increased Oxidative Stress Protection.Journal of proteome research · 2025Article
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- Increasing sustainability and reproducibility ofFrontiers in toxicology · 2024Article
- An original donor-dependent spheroid system for the prediction of idiosyncratic drug-induced liver injury risk.In vitro models · 2023Article
- Dengue activates mTORC2 signaling to counteract apoptosis and maximize viral replication.Frontiers in cellular and infection microbiology · 2022Article
- The Curious Case of the HepG2 Cell Line: 40 Years of Expertise.International journal of molecular sciences · 2021Review
- Preclinical models of idiosyncratic drug-induced liver injury (iDILI): Moving towards prediction.Acta pharmaceutica Sinica. B · 2021Review
- Hepatitis B virus infection modeling using multi-cellular organoids derived from human induced pluripotent stem cells.World journal of gastroenterology · 2021Review
- Application of In Vitro Metabolism Activation in High-Throughput Screening.International journal of molecular sciences · 2020Review
- In Vitro Systems for Studying Different Genotypes/Sub-Genotypes of Hepatitis B Virus: Strengths and Limitations.Viruses · 2020Review
- mRNA levels are buffered upon knockdown of RNA decay and translation factors via adjustment of transcription rates in human HepG2 cells.RNA biology · 2019Article
- Biology and Bias in Cell Type-Specific RNAseq of Nucleus Accumbens Medium Spiny Neurons.Scientific reports · 2019Article
- RNA-seq reveals distinctive RNA profiles of small extracellular vesicles from different human liver cancer cell lines.Oncotarget · 2017Article
- Promises and Challenges of Eco-Physiological Genomics in the Field: Tests of Drought Responses in Switchgrass.Plant physiology · 2016Article
- Transcriptome-Wide Analysis of Hepatitis B Virus-Mediated Changes to Normal Hepatocyte Gene Expression.PLoS pathogens · 2016Article
- Simultaneous, Single-Cell Measurement of Messenger RNA, Cell Surface Proteins, and Intracellular Proteins.Current protocols in cytometry · 2016Article
- The Size of the Human Proteome: The Width and Depth.International journal of analytical chemistry · 2016Review
Corrections and comments
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Authors and funding
14 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHuman hepatoma HepG2 cells are used as an in vitro model of the human liver. High-throughput transcriptomic sequencing is an advanced approach for assessing the functional state of a tissue or cell type. However, the influence of experimental factors, such as the sample preparation method and inter-laboratory variation, on the transcriptomic profile has not been evaluated.
resultsThe whole-transcriptome sequencing of HepG2 cells was performed using the SOLiD platform and validated using droplet digital PCR. The gene expression profile was compared to the results obtained with the same sequencing method in another laboratory and using another sample preparation method. We also compared the transcriptomic profile HepG2 cells with that of liver tissue. Comparison of the gene expression profiles between the HepG2 cell line and liver tissue revealed the highest variation, followed by HepG2 cells submitted to two different sample preparation protocols. The lowest variation was observed between HepG2 cells prepared by two different laboratories using the same protocol. The enrichment analysis of the genes that were differentially expressed between HepG2 cells and liver tissue mainly revealed the cancer-associated gene signature of HepG2 cells and the activation of the response to chemical stimuli in the liver tissue. The HepG2 transcriptome obtained with the SOLiD platform was highly correlated with the published transcriptome obtained with the Illumina and Helicos platforms, with moderate correspondence to microarrays.
conclusionsIn the present study, we assessed the influence of experimental factors on the HepG2 transcriptome and identified differences in gene expression between the HepG2 cell line and liver cells. These findings will facilitate robust experimental design in the fields of pharmacology and toxicology. Our results were supported by a comparative analysis with previous HepG2 gene expression studies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.