ArticleMolecular pathology : MP2003
Validation of cDNA microarray gene expression data obtained from linearly amplified RNA.
Article in Molecular pathology : MP, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
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- Early pregnancy peripheral blood gene expression and risk of preterm delivery: a nested case control study.BMC pregnancy and childbirth · 2009Article
- Molecular profiling of experimental endometriosis identified gene expression patterns in common with human disease.Fertility and sterility · 2007Article
- Comparative expression profiling in meristems of inbred-hybrid triplets of maize based on morphological investigations of heterosis for plant height.Plant molecular biology · 2007Article
- Melatonin treatment in old mice enables a more youthful response to LPS in the brain.Journal of neuroimmunology · 2007Article
- Evaluation of global RNA amplification and its use for high-throughput transcript analysis of laser-microdissected endosperm.International journal of plant genomics · 2007Article
- Biologically relevant effects of mRNA amplification on gene expression profiles.BMC bioinformatics · 2006Article
- Loss of parasympathetic innervation leads to sustained expression of pro-inflammatory genes in the rat lacrimal gland.Autonomic neuroscience : basic & clinical · 2006Article
- Characterization of a method for profiling gene expression in cells recovered from intact human prostate tissue using RNA linear amplification.Prostate cancer and prostatic diseases · 2006Article
- Comparative evaluation of linear and exponential amplification techniques for expression profiling at the single-cell level.Genome biology · 2006Article
- Global gene expression profiles reveal significant nuclear reprogramming by the blastocyst stage after cloning.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Article
- aRNA-longSAGE: a new approach to generate SAGE libraries from microdissected cells.Nucleic acids research · 2004Article
- miRNA Expression in Ovarian Cancer in Fresh Frozen, Formalin-fixed Paraffin-embedded and Plasma Samples.In vivo (Athens, Greece)Article
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Abstract
backgroundDNA microarray technology has permitted the analysis of global gene expression profiles for several diseases, including cancer. However, standard hybridisation and detection protocols require micrograms of mRNA for microarray analysis, limiting broader application of this technology to small excisional biopsies, needle biopsies, and/or microdissected tissue samples. Therefore, linear amplification protocols to increase the amount of RNA have been developed. The correlation between the results of microarray experiments derived from non-amplified RNA and amplified samples needs to be evaluated in detail.
methodsTotal RNA was amplified and replicate hybridisation experiments were performed with linearly amplified (aRNA) and non-amplified mRNA from tonsillar B cells and the SUDHL-6 cell line using cDNA microarrays containing approximately 4500 genes. The results of microarray differential expression using either source of RNA (mRNA or aRNA) were also compared with those found using real time quantitative reverse transcription polymerase chain reaction (QRT-PCR).
resultsMicroarray experiments using aRNA generated reproducible data displaying only small differences to data obtained from non-amplified mRNA. The quality of the starting total RNA template and the concentration of the promoter primer used to synthesise cDNA were crucial components of the linear amplification reaction. Approximately 80% of selected upregulated and downregulated genes identified by microarray analysis using linearly amplified RNA were confirmed by QRT-PCR using non-amplified mRNA as the starting template.
conclusionsLinear RNA amplification methods can be used to generate high fidelity microarray expression data of comparable quality to data generated by microarray methods that use non-amplified mRNA samples.
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