two-color microarray-based gene expression analysis microarrays  (Agilent technologies)

Journal: Frontiers in Oncology

Article Title: Oncopig bladder cancer cells recapitulate human bladder cancer treatment responses in vitro

doi: 10.3389/fonc.2024.1323422

Figure Lengend Snippet: Summary of apoptosis pathways in human and Oncopig cells. Summarized apoptotic pathways altered by gemcitabine treatment in Oncopig BCCL and 5637 cells evaluated by microarray. There were multiple possible cellular pathways involved in apoptosis induction, such as: TP53INP1/P53/BCL/BAX/CASPASE mitochondrial intrinsical pathway; TP53INP1/TP73 activation; FAS/RB1/GADD45B/CASPASE pathway and cell rounding up by RND1 and/or ZMYM6.

Article Snippet: To obtain the gene transcription panel of treated and untreated human and Oncopig cells, the Two-Color Microarray-Based Gene Expression Analysis microarrays (Agilent Technologies Inc, Santa Clara, CA, USA) were used according to the manufacturer’s instructions.

Techniques: Microarray, Activation Assay

Journal: PLoS ONE

Article Title: A Conditional Mouse Mutant in the Tumor Suppressor SdhD Gene Unveils a Link between p21 WAF1/Cip1 Induction and Mitochondrial Dysfunction

doi: 10.1371/journal.pone.0085528

Figure Lengend Snippet: A. SdhD mRNA levels in heterozygous (+/−) and SDHD-ESR adrenal medulla and kidney relative to wild-type (+/+) tissues 7 days after the start of the tamoxifen treatment, as obtained from the corresponding microarray feature (Gene Bank accession n° NM_025848). *, P ≤0.05; ***, P ≤0.001. The number of samples is 8 per group. B. Supervised hierarchical clustering of adrenal medulla (AM) and kidney samples based on genes that showed significant differences in their expression level. The heatmap and the hierarchical tree are shown for 8 samples, grouped in pairs, per genotype.

Article Snippet: For microarray analysis, 200 ng (kidney) or 45 ng (adrenal medulla) of RNA were reverse-transcribed into cRNA and labeled with the Two-Color Microarray Low Input Quick Amp Labeling Kit (Agilent Technologies).

Techniques: Microarray, Expressing

Journal: PLoS ONE

Article Title: A Conditional Mouse Mutant in the Tumor Suppressor SdhD Gene Unveils a Link between p21 WAF1/Cip1 Induction and Mitochondrial Dysfunction

doi: 10.1371/journal.pone.0085528

Figure Lengend Snippet: A. Comparative functional analysis of datasets generated from adrenal medulla (AM) and kidney samples from SDHD-ESR mice. The significance of each molecular and cellular function is indicated by –log of the p-value. B. Quantitative RT-PCR of RNA samples used in the microarray study based on specific primers for amplification of the Cdkn1a mRNA.

Article Snippet: For microarray analysis, 200 ng (kidney) or 45 ng (adrenal medulla) of RNA were reverse-transcribed into cRNA and labeled with the Two-Color Microarray Low Input Quick Amp Labeling Kit (Agilent Technologies).

Techniques: Functional Assay, Generated, Cell Function Assay, Quantitative RT-PCR, Microarray, Amplification

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