» Articles » PMID: 18554498

The Normalization of Gene Expression Data in Melanoma: Investigating the Use of Glyceraldehyde 3-phosphate Dehydrogenase and 18S Ribosomal RNA As Internal Reference Genes for Quantitative Real-time PCR

Overview
Journal Anal Biochem
Publisher Elsevier
Specialty Biochemistry
Date 2008 Jun 17
PMID 18554498
Citations 19
Authors
Affiliations
Soon will be listed here.
Abstract

We examined a panel of 26 melanoma and fibroblast samples (tissues and cultured cells) to evaluate the suitability of two commonly used housekeeping genes, glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and 18S ribosomal RNA (rRNA), for quantitative real-time PCR. Both genes showed significant variations within the individual cell line and tissue groups. Although no overall trends were observed in the expression of the 18S rRNA, GAPDH was up-regulated in melanoma tissue and cultured cells compared with the corresponding normal samples. In melanoma and fibroblast cell lines and tissues, absolute quantification appears to be more appropriate than normalizing messenger RNA (mRNA) expression via GAPDH or 18S rRNA housekeeping genes.

Citing Articles

Genome-Wide Analysis of the PYL Gene Family in and Its Responses to Abiotic Stresses.

Yu J, Wang R, Zhang X, Chen S Int J Mol Sci. 2025; 25(24.

PMID: 39769490 PMC: 11678367. DOI: 10.3390/ijms252413728.


Genome-Wide Identification and Characterization of WRKY Transcription Factors in Suk. and Their Responses to Abiotic Stresses.

Yu J, Zhang X, Cao J, Bai H, Wang R, Wang C Int J Mol Sci. 2023; 24(19).

PMID: 37834448 PMC: 10573109. DOI: 10.3390/ijms241915000.


Genome-Wide Identification and Expression Profiles of C-Repeat Binding Factor Transcription Factors in under Abiotic Stress.

Zhang X, Yu J, Wang R, Liu W, Chen S, Wang Y Int J Mol Sci. 2023; 24(13).

PMID: 37445753 PMC: 10342014. DOI: 10.3390/ijms241310573.


A Strategy for the Selection of RT-qPCR Reference Genes Based on Publicly Available Transcriptomic Datasets.

Nevone A, Lattarulo F, Russo M, Panno G, Milani P, Basset M Biomedicines. 2023; 11(4).

PMID: 37189697 PMC: 10135859. DOI: 10.3390/biomedicines11041079.


Quantification of Human Epidermal Growth Factor Receptor 2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded and Frozen Breast Cancer Tissues.

Kennedy J, Whiteaker J, Kennedy L, Bosch D, Lerch M, Schoenherr R Clin Chem. 2021; 67(7):1008-1018.

PMID: 34136904 PMC: 8260184. DOI: 10.1093/clinchem/hvab047.


References
1.
Hoek K . DNA microarray analyses of melanoma gene expression: a decade in the mines. Pigment Cell Res. 2007; 20(6):466-84. DOI: 10.1111/j.1600-0749.2007.00412.x. View

2.
Meijerink J, Mandigers C, van de Locht L, Tonnissen E, Goodsaid F, Raemaekers J . A novel method to compensate for different amplification efficiencies between patient DNA samples in quantitative real-time PCR. J Mol Diagn. 2001; 3(2):55-61. PMC: 1910699. DOI: 10.1016/S1525-1578(10)60652-6. View

3.
Butte A, Dzau V, Glueck S . Further defining housekeeping, or "maintenance," genes Focus on "A compendium of gene expression in normal human tissues". Physiol Genomics. 2002; 7(2):95-6. DOI: 10.1152/physiolgenomics.2001.7.2.95. View

4.
Goidin D, Mamessier A, Staquet M, Schmitt D, Berthier-Vergnes O . Ribosomal 18S RNA prevails over glyceraldehyde-3-phosphate dehydrogenase and beta-actin genes as internal standard for quantitative comparison of mRNA levels in invasive and noninvasive human melanoma cell subpopulations. Anal Biochem. 2001; 295(1):17-21. DOI: 10.1006/abio.2001.5171. View

5.
Nolan T, Hands R, Bustin S . Quantification of mRNA using real-time RT-PCR. Nat Protoc. 2007; 1(3):1559-82. DOI: 10.1038/nprot.2006.236. View