Background: Human hepatoma HepG2 cells are used as an in vitro model of the human liver. High-throughput\ntranscriptomic sequencing is an advanced approach for assessing the functional state of a tissue or cell type. However,\nthe influence of experimental factors, such as the sample preparation method and inter-laboratory variation, on the\ntranscriptomic profile has not been evaluated.\nResults: The whole-transcriptome sequencing of HepG2 cells was performed using the SOLiD platform and validated\nusing droplet digital PCR. The gene expression profile was compared to the results obtained with the same sequencing\nmethod in another laboratory and using another sample preparation method. We also compared the transcriptomic\nprofile HepG2 cells with that of liver tissue. Comparison of the gene expression profiles between the HepG2 cell line\nand liver tissue revealed the highest variation, followed by HepG2 cells submitted to two different sample preparation\nprotocols. The lowest variation was observed between HepG2 cells prepared by two different laboratories using the\nsame protocol. The enrichment analysis of the genes that were differentially expressed between HepG2 cells and liver\ntissue mainly revealed the cancer-associated gene signature of HepG2 cells and the activation of the response to\nchemical stimuli in the liver tissue. The HepG2 transcriptome obtained with the SOLiD platform was highly correlated\nwith the published transcriptome obtained with the Illumina and Helicos platforms, with moderate correspondence\nto microarrays.\nConclusions: In the present study, we assessed the influence of experimental factors on the HepG2 transcriptome and\nidentified differences in gene expression between the HepG2 cell line and liver cells. These findings will facilitate robust\nexperimental design in the fields of pharmacology and toxicology. Our results were supported by a comparative\nanalysis with previous HepG2 gene expression studies.
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