Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis.

Adel M. Talaat, Susan T. Howard, Walker Hale, Rick Lyons, Harold Garner, Stephen Johnston

Research output: Contribution to journalArticle

148 Citations (Scopus)

Abstract

A fundamental problem in DNA microarray analysis is the lack of a common standard to compare the expression levels of different samples. Several normalization protocols have been proposed to overcome variables inherent in this technology. As yet, there are no satisfactory methods to exchange gene expression data among different research groups or to compare gene expression values under different stimulus-response profiles. We have tested a normalization procedure based on comparing gene expression levels to the signals generated from hybridizing genomic DNA (genomic normalization). This procedure was applied to DNA microarrays of Mycobacterium tuberculosis using RNA extracted from cultures growing to the logarithmic and stationary phases. The applied normalization procedure generated reproducible measurements of expression level for 98% of the putative mycobacterial ORFs, among which 5.2% were significantly changed comparing the logarithmic to stationary growth phase. Additionally, analysis of expression levels of a subset of genes by real time PCR technology revealed an agreement in expression of 90% of the examined genes when genomic DNA normalization was applied instead of 29-68% agreement when RNA normalization was used to measure the expression levels in the same set of RNA samples. Further examination of microarray expression levels displayed clusters of genes differentially expressed between the logarithmic, early stationary and late stationary growth phases. We conclude that genomic DNA standards offer advantages over conventional RNA normalization procedures and can be adapted for the investigation of microbial genomes.

Original languageEnglish (US)
JournalNucleic Acids Research
Volume30
Issue number20
StatePublished - Oct 15 2002
Externally publishedYes

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Gene Expression Profiling
Mycobacterium tuberculosis
RNA
DNA
Oligonucleotide Array Sequence Analysis
Gene Expression
Microbial Genome
Technology
Microarray Analysis
Multigene Family
Growth
Open Reading Frames
Genes
Real-Time Polymerase Chain Reaction
Research

ASJC Scopus subject areas

  • Genetics

Cite this

Talaat, A. M., Howard, S. T., Hale, W., Lyons, R., Garner, H., & Johnston, S. (2002). Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis. Nucleic Acids Research, 30(20).

Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis. / Talaat, Adel M.; Howard, Susan T.; Hale, Walker; Lyons, Rick; Garner, Harold; Johnston, Stephen.

In: Nucleic Acids Research, Vol. 30, No. 20, 15.10.2002.

Research output: Contribution to journalArticle

Talaat, AM, Howard, ST, Hale, W, Lyons, R, Garner, H & Johnston, S 2002, 'Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis.', Nucleic Acids Research, vol. 30, no. 20.
Talaat, Adel M. ; Howard, Susan T. ; Hale, Walker ; Lyons, Rick ; Garner, Harold ; Johnston, Stephen. / Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis. In: Nucleic Acids Research. 2002 ; Vol. 30, No. 20.
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