two-color microarray platform  (Agilent technologies)

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

Journal: PeerJ

Article Title: Identifying genes and regulatory pathways associated with the scleractinian coral calcification process

doi: 10.7717/peerj.3590

Figure Lengend Snippet: Eight fragments of Stylophora pistillata were incubated in calcium seawater (SW) concentrations of seawater plus 100 mg/L calcium (SW + 100) and plus 200 mg/L calcium (SW + 200) during daytime (11:00) and during night-time (23:00). In each sampling time, four replicates were analyzed for calcification rates and four replicates from SW and SW+100 treatments, for microarray analysis.

Article Snippet: Total RNA was labeled and hybridized against custom S. pistillata microarray; an Agilent two-color gene expression microarray platform with 8 × 15 K probe per slide; microarray samples included four SW+100 and four SW (control) samples for each time point (11:00 and 23:00).

Techniques: Incubation, Sampling, Microarray

Journal:

Article Title: CLIMBING FIBERS INDUCE microRNA TRANSCRIPTION IN CEREBELLAR PURKINJE CELLS

doi: 10.1016/j.neuroscience.2010.09.039

Figure Lengend Snippet: Three groups of three mice received binocular HOKS for 24 h in the P→A direction with respect to the right eye. Total RNA was extracted from the left and right flocculi of each mouse and combined for each group. The RNA from each group was analyzed on a miRNA microarray, and subsequently combined for analysis. A. Each data point in the Volcano plot represents four variables: 1) The fold change for each miRNA is represented on abscissa (right floc./left floc), 2) Statistical probability transcription difference (p-value) of a miRNA between the left and right flocculi is represented on left ordinate, 3) Average copy number (color coded) is represented on right ordinate and 4) Frequency of occurrence a miRNA relative to all other sampled miRNAs is represented as data point diameter. B. Twelve miRNAs were screened using three criteria: 1) A fold change >2, 2) A p-value <0.005, and 3) An average copy number >256. Error bars indicate standard error of the mean. Histogram color indicates copy number according to the right ordinate in A.

Article Snippet: The spindle shaped mouse flocculus is ~1.1 mm in axial length, ~400 μm at its peak diameter and weighs ~400 μg. miRNA microarray analysis miRNA expression profiling of mouse flocculus was performed using a two-color microarray platform (Asuragen Technical Services, Austin, TX).

Techniques: Microarray