Real-time polymerase chain reaction-based exponential sample amplification for microarray gene expression profiling

Zsolt B. Nagy, János Z. Kelemen, Liliána Z. Fehér, A. Zvara, Kata Juhász, L. Puskás

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Conventional approaches to target labeling for gene expression analysis using microarray technology typically require relatively large amounts of RNA, a serious limitation when the available sample is limited. Here we describe an alternative exponential sample amplification method by using quantitative real-time polymerase chain reaction (QRT-PCR) to follow the amplification and eliminate the overamplified cDNA which could distort the quantitative ratio of the starting mRNA population. Probes generated from nonamplified, PCR-amplified, and real-time-PCR-amplified cDNA samples were generated from lipopolysaccharide-treated and nontreated mouse macrophages and hybridized to mouse cDNA microarrays. Signals obtained from the three protocols were compared. Reproducibility and reliability of the methods were determined. The Pearson correlation coefficients for replica experiments were r = 0.927 and r = 0.687 for QRT-PCR-amplification and PCR-overamplification protocols, respectively. χ 2 test showed that overamplification resulted in major biases in expression ratios, while these alterations could be eliminated by following the cycling status with QRT-PCR. Our exponential sample amplification protocol preserves the original expression ratios and allows unbiased gene expression analysis from minute amounts of starting material.

Original languageEnglish
Pages (from-to)76-83
Number of pages8
JournalAnalytical Biochemistry
Volume337
Issue number1
DOIs
Publication statusPublished - Feb 1 2005

Fingerprint

Polymerase chain reaction
Gene Expression Profiling
Microarrays
Gene expression
Amplification
Real-Time Polymerase Chain Reaction
Complementary DNA
Gene Expression
Polymerase Chain Reaction
Macrophages
Microarray Analysis
Oligonucleotide Array Sequence Analysis
Labeling
Lipopolysaccharides
RNA
Technology
Messenger RNA
Population
Experiments

Keywords

  • Exponential sample amplification
  • Gene expression profiling
  • Microarray
  • Quantitative real-time PCR

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Molecular Biology

Cite this

Real-time polymerase chain reaction-based exponential sample amplification for microarray gene expression profiling. / Nagy, Zsolt B.; Kelemen, János Z.; Fehér, Liliána Z.; Zvara, A.; Juhász, Kata; Puskás, L.

In: Analytical Biochemistry, Vol. 337, No. 1, 01.02.2005, p. 76-83.

Research output: Contribution to journalArticle

Nagy, Zsolt B. ; Kelemen, János Z. ; Fehér, Liliána Z. ; Zvara, A. ; Juhász, Kata ; Puskás, L. / Real-time polymerase chain reaction-based exponential sample amplification for microarray gene expression profiling. In: Analytical Biochemistry. 2005 ; Vol. 337, No. 1. pp. 76-83.
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