whole mouse genome oligo microarray kit  (SuperArray Bioscience Corporation)

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

Journal: Frontiers in Cardiovascular Medicine

Article Title: Cardiac immune cell infiltration associates with abnormal lipid metabolism

doi: 10.3389/fcvm.2022.948332

Figure Lengend Snippet: CD36 deletion associates with markers of inflammation in heart tissue and isolated macrophages. (A) Microarray analysis in CD36 –/– heart shows upregulated biological pathways involved in immune cell activation and inflammation ( n = 3/group). Pathway analysis obtained from Reactome analysis database using differentially regulated genes (>1.6 or <0.7). Number of differentially regulated genes is indicated on the significance bar for each pathway. (B) WT bone marrow-derived macrophages (BMDM) were subjected to a polarization protocol to yield M1- and M2-like macrophages and were assayed for CD36 expression levels by western blotting. WT M1- and M2-like macrophages were assayed for the content of (C) PGD2 and (D) 5-HEPE at baseline and following DHA or LA treatment. (E–G) BMDM were obtained from WT or CD36 –/– mice and subjected to the polarization protocol. M1- and M2-like macrophages were then treated with DHA or LA to measure the content of (E) PGD2, (F) the DHA metabolite 17-Hydroxy-ocosahexaenoic acid (17-HDHA) and (G) the linoleic acid metabolite 13-Hydroxyoctadecadienoic acid (13-HODE). Eicosanoids were measured by LC–MS. All data ( n = 4/group) are means ± SE with n representing the number of mice per group. Statistical significance is determined by Student’s t test. * p < 0.05.

Article Snippet: Microarray analyses were performed using the Whole Mouse Genome Oligo Microarray Kit (Agilent Technologies, Santa Clara, CA).

Techniques: Isolation, Microarray, Activation Assay, Derivative Assay, Expressing, Western Blot, Liquid Chromatography with Mass Spectroscopy