whole mouse genome oligo microarray (4 44 k  (Agilent technologies)

Journal: PLoS ONE

Article Title: Androgen-Responsive MicroRNAs in Mouse Sertoli Cells

doi: 10.1371/journal.pone.0041146

Figure Lengend Snippet: ( A ) Heat map representation of miRNA microarray analyses on total RNA isolated from purified Sertoli cells from control (Sham), flutamide-acyline-treated (Flut+Acy), and flutamide-acyline testosterone-replacement (Flut+Acy+T) mice. Green or red color on the heat map indicates a decrease or increase of miRNA level, respectively, and color intensities correspond to relative signal levels on a logarithmic scale. Sertoli cells were pooled from six mice for each group. ( B ) Real-time RT-PCR analysis (on RNA from purified Sertoli cells) of selected miRNAs using miRNA-specific primers. Shown are selected miRNAs with increased and decreased expression in the absence of androgen and rescued to control levels by testosterone-replacement in the microarray analysis. We pooled Sertoli cells from six mice for each group for each experiment ( n = 4 for upregulated miRNAs and n = 3 for downregulated miRNAs). ( C ) Real-time RT-PCR analysis on RNA from purified Sertoli cells from LHβ KO and sibling control mice ( n = 3; four mice each) for selected miRNAs. ( D ) Real-time RT-PCR analysis of selected miRNA expression on RNA isolated from Sertoli cells from Sham, Flut+Acy, or Flut+Acy+T mice for indicated days. Results are mean of three different experiments. We pooled Sertoli cells from six mice for each group for each time point. All values for B – D are normalized against RNU19 levels.

Article Snippet: We hybridized purified Sertoli cell RNA to the Agilent 4×44 k Whole Mouse Genome Microarray (Agilent Technologies, Santa Clara, CA) according to manufacturer's protocol and scanned with the Agilent G2505B scanner.

Techniques: Microarray, Isolation, Purification, Quantitative RT-PCR, Expressing

Journal: Advances in Pharmacological Sciences

Article Title: Chronic Treatment with a Promnesiant GABA-A α 5-Selective Inverse Agonist Increases Immediate Early Genes Expression during Memory Processing in Mice and Rectifies Their Expression Levels in a Down Syndrome Mouse Model

doi: 10.1155/2011/153218

Figure Lengend Snippet: PCA on three-copy genes from Ts65Dn mice measured on microarrays. The first two principal components discriminated between euploid and Ts65Dn mice.

Article Snippet: After purification and quantification on a Nanoview (ThermoFisher Scientific), 2 μ g of each Cy3-cRNA were hybridized overnight on Whole Mouse Genome 4 × 44 K v1 Microarrays (Agilent Technologies) according to the manufacturer's instructions.

Techniques:

Journal: Advances in Pharmacological Sciences

Article Title: Chronic Treatment with a Promnesiant GABA-A α 5-Selective Inverse Agonist Increases Immediate Early Genes Expression during Memory Processing in Mice and Rectifies Their Expression Levels in a Down Syndrome Mouse Model

doi: 10.1155/2011/153218

Figure Lengend Snippet: PCA on IEGs expression measured on microarrays. The first principal component fully discriminated euploid and Ts65Dn mice. The second principal component partially discriminated vehicle- and α 5IA-treated mice.

Article Snippet: After purification and quantification on a Nanoview (ThermoFisher Scientific), 2 μ g of each Cy3-cRNA were hybridized overnight on Whole Mouse Genome 4 × 44 K v1 Microarrays (Agilent Technologies) according to the manufacturer's instructions.

Techniques: Expressing

Journal: BMC Genomics

Article Title: Species-specific regulation of PXR/CAR/ER-target genes in the mouse and rat liver elicited by o , p' -DDT

doi: 10.1186/1471-2164-9-487

Figure Lengend Snippet: Microarray and QRT-PCR results . (A) Identification of differentially regulated genes. (B) Number of differentially expressed genes following o , p' -DDT treatment in the mouse liver. Differentially expressed genes were selected based on a p1( t ) ≥ 0.999 at two or more time points and an absolute fold change ≥ 1.5 at one or more time points relative to time-matched vehicle controls. All differentially expressed genes are listed in Additional file . (C) Verification of microarray results by QRT-PCR. QRT-PCR results relative to time-matched vehicle controls are shown as bar and presented as mean ± SE. Microarray results are represented as lines. The dashed line indicates the expression level of the time-matched vehicle control. The asterisk (*) indicates a significant ( p < 0.05) difference from the time-matched vehicle controls for QRT-PCR, n = 5. (D) Hepatic expression of PXR/CAR-target genes in o , p' -DDT-treated mouse. A heat map of o , p' -DDT elicited microarray expression profiles for selected PXR-, CAR-specific and PXR/CAR-shared target genes identified in the literature [ - ]. While some CAR-regulated genes such as Cyp1a1 , Fmo5 , Sult1d1 or Abcc2 were moderately induced, several PXR-target genes, including ApoA4 , Ces2 , Gstm2 or Insig2 , exhibited strong induction. However, other PXR-target genes such as Hmgcs1 and Hmgcs2 were down-regulated.

Article Snippet: Whole Mouse Genome 4 × 44 K Oligo Microarray Kit (Agilent Technologies, Inc, Santa Clara, CA) was used for global gene expression analysis.

Techniques: Microarray, Quantitative RT-PCR, Expressing

Journal: BMC Genomics

Article Title: Species-specific regulation of PXR/CAR/ER-target genes in the mouse and rat liver elicited by o , p' -DDT

doi: 10.1186/1471-2164-9-487

Figure Lengend Snippet: Selected microarray results

Article Snippet: Whole Mouse Genome 4 × 44 K Oligo Microarray Kit (Agilent Technologies, Inc, Santa Clara, CA) was used for global gene expression analysis.

Techniques: Microarray

Journal: BMC Genomics

Article Title: Species-specific regulation of PXR/CAR/ER-target genes in the mouse and rat liver elicited by o , p' -DDT

doi: 10.1186/1471-2164-9-487

Figure Lengend Snippet: Comparative analysis of global gene expression profiles elicited by o , p '-DDT . (A). Comparative gene expression analysis between EE-treated mouse, o , p' -DDT-treated rat and o , p' -DDT-treated mouse. A total of 996 orthologs were represented on the rat cDNA microarray, mouse cDNA microarray and mouse Agilent oligonucleotide microarrays determined by HomoloGene . 538 of these orthologs showed a |fold change| ≥ 1.5 for at least one time point in either species. These 538 differentially expressed orthologs were subjected to hierarchical clustering. The dendrogram illustrates that mouse o , p' -DDT gene expression profiles are more similar to rat o , p' -DDT gene expression profiles than the mouse EE gene expression profiles. (B) Correlation analysis using differentially expressed orthologous genes. The temporal profiles of o , p' -DDT-treated mouse liver (current study) and those of the o , p' -DDT-treated rat liver were compared by determining the Pearson's correlation of the temporal gene expression (fold change) and significance (p1 [ t ] value) between orthologs. Both studies used comparable study designs and data analysis methods, although different platforms were used (i.e., rat cDNA microarray and mouse Agilent oligonucleotide microarray). 140 genes were identified as differentially expressed orthologs. (C) Scatter plot of the 140 differentially expressed orthologous genes. Correlations for gene expression and significance approaching 1.0 indicate that the behavior or the orthologous genes are similar and would fall in the upper right quadrant. Orthologs tended to localize in upper- or lower-right quadrant (32.9% and 47.9% of total number of spots, respectively), indicating that temporal gene expression changes for o , p' -DDT-treated mouse and rat liver are comparable. However, poor correlations between the temporal p1( t ) values and gene expression fold changes would fall within the lower left quadrant. For example, Cyp17a1 fell into this quadrant suggesting that significant differences exist between the rat and mouse ortholog expression profiles.

Article Snippet: Whole Mouse Genome 4 × 44 K Oligo Microarray Kit (Agilent Technologies, Inc, Santa Clara, CA) was used for global gene expression analysis.

Techniques: Expressing, Microarray

Journal: BMC Genomics

Article Title: Species-specific regulation of PXR/CAR/ER-target genes in the mouse and rat liver elicited by o , p' -DDT

doi: 10.1186/1471-2164-9-487

Figure Lengend Snippet: Species-specific regulation of steroid hormone metabolism elicited by o , p '-DDT . (A) Overview of the role of CYP17A1 and CYP7B1 in steroid metabolism. CYP17A1 metabolizes pregnenolone and progesterone to produce DHEA and androstenedione, respectively. Hepatic CYP7B1 is involved in bile acid biosynthesis, and also responsible for 7α-hydroxylation of DHEA. (B) Hepatic Cyp17a1 and (C) Cyp7b1 mRNA levels in the o , p' -DDT-treated mouse and rat. QRT-PCR results relative to time-matched vehicle controls are shown as bars and presented as mean ± SE. Microarray results are represented as lines. o , p' -DDT induced Cyp17a1 and Cyp7b1 mRNAs in the mouse liver, while it did not affect in the rat liver . The dashed line indicates the expression level of the time-matched vehicle control. The asterisk (*) indicates a significant ( p < 0.05) difference from the time-matched vehicle controls for QRT-PCR, n = 5. (C) Representative Western analysis result for hepatic CYP17A1 protein in o , p' -DDT-treated mouse liver. CYP17A1 protein levels were induced at 18 and 24 h. Western analyses were performed on 3 independent biological replicates to verify the consistency of the results. C , control; T , 300 mg/kg o , p' -DDT. (D) Blood DHEA-S levels. DHEA-S level was significantly higher at 12 h following o , p' -DDT treatment compared to time-matched controls in the mouse, while it did not change in rats.

Article Snippet: Whole Mouse Genome 4 × 44 K Oligo Microarray Kit (Agilent Technologies, Inc, Santa Clara, CA) was used for global gene expression analysis.

Techniques: Quantitative RT-PCR, Microarray, Expressing, Western Blot