Technical analysis of cDNA microarrays

Cinda P. Scott, Jeff VanWye, Danielle M Mcdonald, Douglas L Crawford

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Background: There is extensive variation in gene expression among individuals within and between populations. Accurate measures of the variation in mRNA expression using microarrays can be confounded by technical variation, which includes variation in RNA isolation procedures, day of hybridization and methods used to amplify and dye label RNA for hybridization. Methodology/Principal Findings: In this manuscript we analyze the relationship between the amount of mRNA and the fluorescent signal from the microarray hybridizations demonstrating that for a wide-range of mRNA concentrations the fluorescent signal is a linear function of the amount of mRNA. Additionally, the separate isolation, labeling or hybridization of RNA does not add significant amounts of variation in microarray measures of gene expression. However, single or double rounds of amplification for labeling do have small but significant affects on 10% of genes, but this source of technical variation is easy to avoid. To examine both technical and stochastic biological variation, mRNA expression was measured from the same five individuals over a six-week time course. Conclusion: There were few, if any, meaningful differences in gene expression among time points. Thus, microarray measures using standard laboratory procedures can be precise and quantitative and are not subject to significant random biological noise.

Original languageEnglish
Article numbere4486
JournalPLoS One
Volume4
Issue number2
DOIs
StatePublished - Feb 16 2009

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Microarrays
Oligonucleotide Array Sequence Analysis
Complementary DNA
nucleic acid hybridization
gene expression
Messenger RNA
Gene expression
microarray technology
RNA
Gene Expression
Labeling
dyes
hybridization
Amplification
Noise
Labels
methodology
Coloring Agents
Genes
genes

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Technical analysis of cDNA microarrays. / Scott, Cinda P.; VanWye, Jeff; Mcdonald, Danielle M; Crawford, Douglas L.

In: PLoS One, Vol. 4, No. 2, e4486, 16.02.2009.

Research output: Contribution to journalArticle

Scott, Cinda P. ; VanWye, Jeff ; Mcdonald, Danielle M ; Crawford, Douglas L. / Technical analysis of cDNA microarrays. In: PLoS One. 2009 ; Vol. 4, No. 2.
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