Journal: PLoS ONE

Article Title: Confounding Factors in the Transcriptome Analysis of an In-Vivo Exposure Experiment

doi: 10.1371/journal.pone.0145252

Figure Lengend Snippet: A: PCA plot of all genes using the untreated WT samples. Indicated are Subsets I and II, with 155 and 109 genes respectively. Red, genes in Subset I that are also in Cluster SC-A. Blue, genes in Subset II that are also in Cluster SC-B; B: A heatmap of microarray signals in all untreated WT samples of the top 5,000 genes with the biggest variance over the whole experiment. The five Sample-Composition and one Time-of-Day specific clusters as explained in the main text are indicated. C: Zoom-in of the five Sample-Composition clusters to reveal the similar expression per cluster over all WT samples.

Article Snippet: After washing, the arrays were scanned with an Agilent DNA microarray scanner (G2565CA, Agilent Technologies) and data was extracted with Feature Extraction software v10.7.3.1 (Agilent Technologies).

Techniques: Microarray, Expressing

Journal: PLoS ONE

Article Title: Study of the Integrated Immune Response Induced by an Inactivated EV71 Vaccine

doi: 10.1371/journal.pone.0054451

Figure Lengend Snippet: A global view of gene modulation in the PBMCs of vaccinated infants (Vac, n = 20), 28 days after the vaccine booster, compared to the placebo cohort (Pla, n = 10) was determined by microarray analysis. The genes were classified according to their function. A heat map representation (a) and principal component analysis (PCA) (b) generated using the significantly modulated genes from at least one comparison versus day 0 are shown. (a) The color scale shows the significantly modulated genes from up- (dark red) to down-regulated (dark blue) to the right of each image. The values are shown on a log 2 scale. (b) The Y value is the log 2 -fold-changes in gene expression of the vaccinated group vs. the placebo group. The up-regulated changes are above the baseline (Y = 0, the same with placebo group), and the down-regulated changes are below the baseline. The bars represent the maximum and minimum. The mean of the fold-changes in gene expression with a 95% CI is shown as the rectangle. The line in the rectangle represents the mean of these fold changes in gene expression. The number of genes that changed after immunization is shown beside the rectangles on the image.

Article Snippet: After hybridization, the microarrays were scanned in the Agilent Microarray Scanner (Cat# G2565CA, Agilent, CA, USA), and the raw data were obtained by Feature Extraction Software 10.7 (Agilent, CA, USA) and normalized using the Quantile algorithm in Gene Spring 11.0 (Agilent, CA, USA).

Techniques: Microarray, Generated, Expressing

Journal: PLoS ONE

Article Title: Study of the Integrated Immune Response Induced by an Inactivated EV71 Vaccine

doi: 10.1371/journal.pone.0054451

Figure Lengend Snippet: Measure of serum proinflammatory cytokines (a) and the modulation of the expression of genes associated with the inflammatory response (b). (a) Levels of serum proinflammatory cytokines in vaccinated and placebo subjects. All cytokine (IL-1b, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10, IL12p70, TNF-α and IFN-γ) levels were measured with an R&D Systems assay kits according to the manufacturer protocol. (b) The genes modulated and associated with the inflammatory response in vaccinated group (Vac) and placebo group (Pla) were classified and fallen under different functional categories: (1) ILs group: IL1A, IL1B, IL2RA, NFKBIZ (activator of IL-6 expression), IL8, IL17C, IL26 and IL32 in the IL group; (2) TNFs group: TNFAIP2 and TNFAIP6; (3) IFNs group: IFNA10 and OAS2 (activator of IFN-γ); (4) chemokines group: CCL3, CCL4, CCL15, CCL23, CCL26, CXCL1, CXCL3 and CXCR7. The levels of gene expression were measured by microarray analysis as described in the Methods. Data are shown in log 2 scale.

Article Snippet: After hybridization, the microarrays were scanned in the Agilent Microarray Scanner (Cat# G2565CA, Agilent, CA, USA), and the raw data were obtained by Feature Extraction Software 10.7 (Agilent, CA, USA) and normalized using the Quantile algorithm in Gene Spring 11.0 (Agilent, CA, USA).

Techniques: Expressing, Functional Assay, Microarray