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Clinical

Performance comparison of Affymetrix and Illumina microarray technologies-GSE11430

Purpose

Cross-platform comparison - The present study was conducted to compare the ability of Affymetrix and Illumina microarray technologies to characterize the differential gene expression profiles of human monocytes and monocyte-derived-macrophages.

Hypothesis

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Experimental Design

Blood samples were obtained from patients with symptoms of acute coronary syndrome who had undergone coronary angiography at the department of cardiology of the Pitié-Salpêtrière Hospital, Paris and who had one stenosis >50 % diagnosed in at least one major coronary artery.RNA samples were extracted from monocyte and monocyte derived macrophage cells. Five biological replicates for each type of sample were hybridized in parallel to the Affymetrix HGU133 plus 2.0 and Illumina Bead Chip Human-6 v1 platforms. In addition, a reference list of differentially expressed genes was generated from a larger number of hybridizations (mRNA from 86 individuals) using a third technology (the academic RNG/MRC two-color chip) and was used as reference to assess the performance of the 2 platforms based on 10 samples. The internal consistency of each platform, the overlap in lists of genes identified as differentially expressed generated on each array type and the biological relevance of significant genes identified on each platform (Gene Ontology (GO) classes enrichments) were assessed.

Experimental Variables

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Controls

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Methods

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Additional Information

Maouche S, Poirier O, Godefroy T, Olaso R et al. Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells. BMC Genomics 2008 Jun 25;9:302. PMID: 18578872

Microarray
Affymetrix HG-U133_Plus_2
10 Samples Loaded: 10
Human (Homo sapiens)
Monocytes , Macrophages
Acute coronary syndrome
Sample Set Spreadsheet
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Samples Preview
Sample ID !Sample_title Age Gender Tissue Cell type
GSM257664 Affy_Monocyte_16 68 male whole blood monocyte
GSM257665 Affy_Macrophage_16 68 male whole blood macrophage
GSM257666 Affy_Monocyte_20 65 male whole blood monocyte
GSM257667 Affy_Macrophage_20 65 male whole blood macrophage
GSM257668 Affy_Monocyte_21 70 male whole blood monocyte
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Log2 Transformed
Raw Signal
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Samples Viewer / Editor

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Sample ID !Sample Title Age Gender Tissue Cell type Patient with symptoms of acute coronary syndrome who had Undergone coronary angiography (who had one stenosis >50 % diagnosed in at least one major coronary artery)
GSM257664
Affy_Monocyte_16
68
male
whole blood
monocyte
True
True
GSM257665
Affy_Macrophage_16
68
male
whole blood
macrophage
True
True
GSM257666
Affy_Monocyte_20
65
male
whole blood
monocyte
True
True
GSM257667
Affy_Macrophage_20
65
male
whole blood
macrophage
True
True
GSM257668
Affy_Monocyte_21
70
male
whole blood
monocyte
True
True
GSM257669
Affy_Macrophage_21
70
male
whole blood
macrophage
True
True
GSM257670
Affy_Monocyte_26
52
male
whole blood
monocyte
True
True
GSM257671
Affy_Macrophage_26
52
male
whole blood
macrophage
True
True
GSM257672
Affy_Monocyte_28
62
male
whole blood
monocyte
True
True
GSM257673
Affy_Macrophage_28
62
male
whole blood
macrophage
True
True

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