Journal: Plant Direct

Article Title: Overexpression of exogenous biuret hydrolase in rice plants confers tolerance to biuret toxicity

doi: 10.1002/pld3.290

Figure Lengend Snippet: Microarray‐based transcriptome analysis in rice suspension cells under biuret toxicity. (a) Biuret toxicity in rice suspension cells. Cells were subcultured into a culture medium supplemented with 0, 0.1, 0.3, and 1.0 mmol/L biuret. Fresh cell weight per culture flask was measured seven days after subcloning. Values are expressed means ± SD ( n = 3). Different alphabets indicate significant differences among groups ( p < 0.05, Tukey's test). (b) Changes in the fresh cell weight over time. Rice cells were subcultured into the culture medium supplemented with 0 and 0.3 mmol/L biuret on day 0. The cells on day three and day 5 were used for subsequent microarray analyses. White circles indicate the control cells, and black circles indicate biuret‐treated cells. Values are expressed means ± SD ( n = 2). An asterisk indicates a significant difference between the treatments ( p < 0.05, t test). (c) Relationship between the normalized average gene expression levels and fold changes of gene expression of the 3‐day‐old biuret‐treated cells to the control cells. Each symbol denotes each microarray spot. Values are geometrical means of two arrays ( n = 2). (d) Relationship between the normalized average gene expression levels and fold changes of gene expression of the 5‐day‐old biuret‐treated cells to the control cells. Each symbol denotes each microarray spot. Eleven points with high non‐significant fold‐change are omitted from the figure. Values are geometrical means of two arrays ( n = 2). (e) Numbers of differentially expressed genes

Article Snippet: Two‐color microarray analysis with two biological replicates was performed using Agilent Rice Oligo DNA Microarray 4x44K slide (Agilent, Santa Clara, CA, USA) according to the manufacturer's instructions to estimate the ratio of transcript abundance between the treatments at each culture period.

Techniques: Microarray, Subcloning, Expressing

Journal: PLoS ONE

Article Title: Expression Profiling of Major Histocompatibility and Natural Killer Complex Genes Reveals Candidates for Controlling Risk of Graft versus Host Disease

doi: 10.1371/journal.pone.0016582

Figure Lengend Snippet: The 20 most strongly regulated non-MHC/non-NKC genes in allogeneic skin explants compared to syngeneic controls as revealed by the microarray experiment.

Article Snippet: After washing, Cy3 and Cy5 intensities were detected by two-color scanning using a DNA microarray scanner (Agilent, G2505B) at 5 micron resolution.

Techniques: Microarray, Sequencing, Derivative Assay

Journal: PLoS ONE

Article Title: Expression Profiling of Major Histocompatibility and Natural Killer Complex Genes Reveals Candidates for Controlling Risk of Graft versus Host Disease

doi: 10.1371/journal.pone.0016582

Figure Lengend Snippet: A subgroup of 8 samples used for the microarray experiment (see Fig. 1 ) was analyzed by qRT-PCR for the expression of 10 MHC and 3 NKC genes. The ΔΔct value was calculated, i.e. the Δct ( Gapdh – gene of interest) of the allogeneic skin explant samples minus Δct ( Gapdh – gene of interest) of the corresponding control sample. The control sample was either a parallel skin explant exposed to syngeneic lymphocytes as in the microarray experiment (syngeneic control, black bars) or a parallel skin explant sample cultured in medium only (medium control, white bars). The means of the ΔΔct values plus standard errors of the mean (SEM) are shown. A positive value indicates an up-regulation of gene expression in the allogeneic samples.

Article Snippet: After washing, Cy3 and Cy5 intensities were detected by two-color scanning using a DNA microarray scanner (Agilent, G2505B) at 5 micron resolution.

Techniques: Microarray, Quantitative RT-PCR, Expressing, Cell Culture

Journal: PLoS ONE

Article Title: MicroRNA Expression Profiles of Whole Blood in Lung Adenocarcinoma

doi: 10.1371/journal.pone.0046045

Figure Lengend Snippet: The scatter-plots show RT-PCR quantification cycle (C q ) values and log 2 -transformed microarray signal values for microRNAs let-7e , miR-22 , miR-30a-5p , miR-185 , miR-210 , and miR-423-5p (n = 11). Pearson correlation coefficients (r) and their 95% confidence intervals and associated P values, and best fitting (least squares) lines are also shown.

Article Snippet: A two-color, oligonucleotide microarray platform from Exiqon® was used to quantify levels of 1282 human microRNAs and 23 human non-microRNAs of <200 nucleotides in the RNA isolated from whole blood specimens.

Techniques: Reverse Transcription Polymerase Chain Reaction, Transformation Assay, Microarray

Journal: PLoS ONE

Article Title: MicroRNA Expression Profiles of Whole Blood in Lung Adenocarcinoma

doi: 10.1371/journal.pone.0046045

Figure Lengend Snippet: A . Unsupervised clustering of the 45 samples of this study by log 2 -transformed microarray signal values of all 395 expressed microRNAs. The numbers indicate identities of the 45 subjects, with cases (n = 22) and controls (n = 23) shown in black and grey, respectively. The sample tree with optimized leaf-ordering is drawn using Pearson correlation for distance metric and average linkage for cluster-to-cluster distance, and the scale for it represents node-heights. B . Supervised clustering of microRNAs by their log 2 -transformed microarray signal values. The heat-map, with the pseudo-color scale underneath, shows log 2 -transformed microarray signal values of the 43 microRNAs whose expression is altered >25% in either direction in the cases compared to the controls. The gene tree is drawn as in A .

Article Snippet: A two-color, oligonucleotide microarray platform from Exiqon® was used to quantify levels of 1282 human microRNAs and 23 human non-microRNAs of <200 nucleotides in the RNA isolated from whole blood specimens.

Techniques: Transformation Assay, Microarray, Expressing

Journal: PLoS ONE

Article Title: MicroRNA Expression Profiles of Whole Blood in Lung Adenocarcinoma

doi: 10.1371/journal.pone.0046045

Figure Lengend Snippet: Dot-plots with medians and inter-quartile ranges of log 2 -transformed microarray signal values for the 22 cases ( black ) and 23 controls ( grey ) are shown for the four microRNAs that are present in a majority of the classifiers generated in internal cross-validation analyses using the linear support vector machines and top-scoring pairs classification methods.

Article Snippet: A two-color, oligonucleotide microarray platform from Exiqon® was used to quantify levels of 1282 human microRNAs and 23 human non-microRNAs of <200 nucleotides in the RNA isolated from whole blood specimens.

Techniques: Transformation Assay, Microarray, Generated, Plasmid Preparation

Journal: PLoS ONE

Article Title: MicroRNA Expression Profiles of Whole Blood in Lung Adenocarcinoma

doi: 10.1371/journal.pone.0046045

Figure Lengend Snippet: A . Receiver operating characteristic curves, the areas under curve ( AUC ) for age, and the line of identity, x = y , with an AUC of 0.5, are shown. B . Correlation with microRNA expression. Values for the clinical variables were correlated with microarray signal values for the 395 expressed microRNAs (n = 45 for age; n = 39 for others). The curves depict frequency histograms of Pearson correlation coefficients ( r ) with a bin of 0.025. Curves were smoothened using four neighbors for averaging and a zero order polynomial. Correlations are also shown for the random variable resampled WBC count for which values were generated by resampling the WBC count data.

Article Snippet: A two-color, oligonucleotide microarray platform from Exiqon® was used to quantify levels of 1282 human microRNAs and 23 human non-microRNAs of <200 nucleotides in the RNA isolated from whole blood specimens.

Techniques: Expressing, Microarray, Generated