microarray assay human genome u133 plus 2.0, genechip® 3’ expression array  (Thermo Fisher)

Journal: PLoS ONE

Article Title: Integrative Discovery of Epigenetically Derepressed Cancer Testis Antigens in NSCLC

doi: 10.1371/journal.pone.0008189

Figure Lengend Snippet: (A) Schematic outline of the integrative epigenetic screening strategy utilized in this study which combined the pharmacologic demethylation of normal cell lines, comparative COPA anaylsis in primary tissue and correlation of gene expression with the epigenetic regulator BORIS in primary tissue. (B) Representative COPA graph of MAGEA12 demonstrating the statistical approach used to find candidate overexpressed CTAs and related genes. Difference in tumor versus normal expression was significant, p value<0.00001 as measured by Mann-Whitney U test. (C) Upfold regulation of mRNA expression in treated normal lung cell lines, NHBE and SAEC, as measured by Affymetrix Human Genome U133 Plus 2.0 mRNA expression platform.

Article Snippet: We carried out oligonucleotide microarray analysis using the GeneChip U133 Plus 2.0 Affymetrix expression microarray (Affymetrix, Santa Clara, CA).

Techniques: Expressing, MANN-WHITNEY

Journal: PLoS ONE

Article Title: Integrative Discovery of Epigenetically Derepressed Cancer Testis Antigens in NSCLC

doi: 10.1371/journal.pone.0008189

Figure Lengend Snippet: (A) Heat map of transcript expression as measured by the Affymetrix Human Genome U133 Plus 2.0 mRNA expression platform. The data were first normalized by setting the mean and standard deviation of each gene to 0 and 1 respectively across all 151 samples. The data were then clustered in the sample domain using hierarchical clustering with average linkage and a Euclidean distance metric. (B) Pearson's correlation coefficient p-value matrix for gene expression which tests for the coexpression of each gene pair across all tumors. This comparison shows the expression correlation of each gene pair in 111 NSCLC. Values to the upper right have been corrected with the Benjamin Hochberg multiple test correction to decrease the false discovery rate; uncorrected values are displayed in the lower left. Shaded cells represent significant p-values.

Article Snippet: We carried out oligonucleotide microarray analysis using the GeneChip U133 Plus 2.0 Affymetrix expression microarray (Affymetrix, Santa Clara, CA).

Techniques: Expressing, Standard Deviation

Journal: International Journal of Molecular Sciences

Article Title: Biomarkers of Periodontitis and Its Differential DNA Methylation and Gene Expression in Immune Cells: A Systematic Review

doi: 10.3390/ijms231912042

Figure Lengend Snippet: Studies on mRNA expression in peripheral blood mononuclear cells (PBMCs) or subcomponents (lymphocytes and monocytes).

Article Snippet: Corbi S.C.T. et al., 2020 [ ] , 24 periodontitis patients for Microarray expression (U133 Plus 2.0, Affimetrix): • 5 poorly controlled T2DM + dyslipidemia + periodontitis (T2DMpoorly-DL-P) • 7 well-controlled T2DM with dyslipidemia and periodontitis (T2DMwell-DL-P) • 6 well-controlled T2DM + dyslipidemia + periodontitis (DL-P) • 6 normoglycemic individuals + dyslipidemia + periodontitis (P) 120 periodontitis patients for RT-qPCR validation of selected DEGs: • 30 T2DMpoorly-DL-P • 30 T2DMwell-DL-P • 30 DL-P • 30 P , For Microarray U133 Plus 2.0: • 6 systemically healthy individuals without periodontitis (H) (homogeneity regarding biochemical, lipid and clinical periodontal parameters). For RT-qPCR validation: - 30 H , Mono-nuclear cells (Lymphocytes and monocytes)/peripheral blood , Expression Microarray U133 Plus 2.0 RT-qPCR (validation) , • P ↓ mRNA IGHG3 ↑ mRNA ITGB2 and HLADRB4. • T2DMpoorly + DL + P ↑ mRNA TGFB1I1 , VNN1 ↓ mRNA HLADRB4 and CXCL8 • T2Dmwell + DL + P ↓ mRNA BPTF , PDE3B ↑ mRNA FN1 • DL + P ↑ mRNA DAB2 ↓ mRNA CD47 and HLADRB4.

Techniques: Expressing, Microarray, Centrifugation, Real-time Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Isolation