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Genomics Inform > Volume 9(3); 2011 > Article
DOI: https://doi.org/10.5808/gi.2011.9.3.127   
Optimized Internal Control and Gene Expression Analysis in Epstein-Barr Virus-Transformed Lymphoblastoid Cell Lines.
Hye Young Nam, Hye Ryun Kim, Sung Mi Shim, Jae Eun Lee, Jun Woo Kim, Hye Kyung Park, Bok Ghee Han, Jae Pil Jeon
National Biobank of Korea, Center for Genome Science, Korea National Institute of Health, Korea Centers for Disease Control & Prevention, Osong Health Technology Administration Complex (OHTAC), Chungbuk 363-951, Korea. jpjeon@cdc.go.kr
Abstract
The Epstein-Barr virus-transformed lymphoblastoid cell line (LCL) is one of the major genomic resources for human genetics and immunological studies. Use of LCLs is currently extended to pharmacogenetic studies to investigate variations in human gene expression as well as drug responses between individuals. We evaluated four common internal controls for gene expression analysis of selected hematopoietic transcriptional regulatory genes between B cells and LCLs. In this study, the expression pattern analyses showed that TBP (TATA box-binding protein) is a suitable internal control for normalization, whereas GAPDH (glyceraldehyde-3-phosphate dehydrogenase) is not a good internal control for gene expression analyses of hematopoiesis-related genes between B cells and LCLs at different subculture passages. Using the TBP normalizer, we found significant gene expression changes in selected hematopoietic transcriptional regulatory genes (downregulation of RUNX1 , RUNX3 , CBFB , TLE1, and NOTCH2; upregulation of MSC and PLAGL2) between B cells and LCLs at different passage numbers. These results suggest that these hematopoietic transcriptional regulatory genes are potential cellular targets of EBV infection, contributing to EBV-mediated B-cell transformation and LCL immortalization.
Keywords: lymphoblastoid cell line; internal control; quantitative real-time polymerase chain reaction
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