Journal: Biochemical and biophysical research communications

Article Title: Genome-wide analysis of murine renal distal convoluted tubular cells for the target genes of mineralocorticoid receptor

doi: 10.1016/j.bbrc.2014.01.125

Figure Lengend Snippet: Validations of MR target genes by ChIP-qPCR and RT-qPCR of the candidate MR target genes. (A) Target sites of ChIP-qPCR (arrow) are shown. The value based on each read number of immunoprecipitated (IP) DNA is visualized as a proportional altitude of each peak. Significantly higher peaks are shown in red, whereas background signals are represented in green. The target site for ChIP-qPCR in the exon 14 of Sgk1 (A, arrowhead) is also shown. 5′ side of DNA is left for the genes shown above the upper number line. The positional relation is inverted for those below the number line. (B) We performed qPCR targeting the genomic DNA shown in A. The ratios of IP DNA and the input DNA are shown. Sgk1 exon14 is used as a negative control for MR-binding. (N = 3, *P < 0.05 each gene vs. control) (also in E). (C) Of 25 genes as shown in Table 1, 5 genes were upregulated by aldosterone (Aldo) for 3 h compared with the control group and inhibited by pretreatment with spironolactone (Spi) (N = 3, *P < 0.05: Aldo vs. control, #P < 0.05: Aldo + Spi vs. Aldo). The results of ChIP-seq (D) and ChIP-qPCR (E) for Ctgf and Serpine1 are also shown in the same manner. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: Microarray mDCT cells with overexpression of 3xFLAG-hMR were incubated with 5 × 10 −6 M spironolactone or vehicle for 2 h, and then with 10 −7 M aldosterone or the same concentration of ethanol for 3 h. mRNA were extracted from the cells treated with ethanol/ethanol (group 1), ethanol/aldosterone (group 2) and spironolactone/aldosterone (group 3) and were analyzed by Affymetrix Mouse Genome 430 2.0 microarrays over 39000 transcripts (Affymetrix, Santa Clara, CA).

Techniques: ChIP-qPCR, Quantitative RT-PCR, Immunoprecipitation, Negative Control, Binding Assay, Control, ChIP-sequencing

Journal: Biochemical and biophysical research communications

Article Title: Genome-wide analysis of murine renal distal convoluted tubular cells for the target genes of mineralocorticoid receptor

doi: 10.1016/j.bbrc.2014.01.125

Figure Lengend Snippet: Overexpression of 3xFLAG-hMR in mDCT cells. (A) A picture of mDCT cells are shown. (B) mRNA of Na-Cl cotransporter (NCC) was expressed in mDCT cells as well as in murine kidney, while not in differentiated mouse podocyte cell line (MPC). GAPDH was used for internal PCR control. (C) Total amounts of 3xFLAG-hMR overexpressed in mDCT cells were analyzed by Western blotting. (D) 3xFLAG-hMR overexpressed in mDCT cells accumulates to the nucleus in response to a physiological dose of aldosterone.

Article Snippet: Microarray mDCT cells with overexpression of 3xFLAG-hMR were incubated with 5 × 10 −6 M spironolactone or vehicle for 2 h, and then with 10 −7 M aldosterone or the same concentration of ethanol for 3 h. mRNA were extracted from the cells treated with ethanol/ethanol (group 1), ethanol/aldosterone (group 2) and spironolactone/aldosterone (group 3) and were analyzed by Affymetrix Mouse Genome 430 2.0 microarrays over 39000 transcripts (Affymetrix, Santa Clara, CA).

Techniques: Over Expression, Control, Western Blot

Journal: Biochemical and biophysical research communications

Article Title: Genome-wide analysis of murine renal distal convoluted tubular cells for the target genes of mineralocorticoid receptor

doi: 10.1016/j.bbrc.2014.01.125

Figure Lengend Snippet: Identification of the candidate MR target genes in mDCT cells by the combination of ChIP-seq and microarray analyses. (A) We compared MR target gene candidates identified by ChIP-seq and microarray analyses. 1414 genes were identified as those determined by GREAT to be associated with MR ChIP-seq peaks, and 186 genes were identified as those upregulated by aldosterone in the microarray. The venn diagram intersection identified 25 genes as MR target gene candidates. (B) MRE/GRE was discovered as de novo motif in MBSs of mDCT cells with the sufficient significance (E-value

Article Snippet: Microarray mDCT cells with overexpression of 3xFLAG-hMR were incubated with 5 × 10 −6 M spironolactone or vehicle for 2 h, and then with 10 −7 M aldosterone or the same concentration of ethanol for 3 h. mRNA were extracted from the cells treated with ethanol/ethanol (group 1), ethanol/aldosterone (group 2) and spironolactone/aldosterone (group 3) and were analyzed by Affymetrix Mouse Genome 430 2.0 microarrays over 39000 transcripts (Affymetrix, Santa Clara, CA).

Techniques: ChIP-sequencing, Microarray

Journal: Oncotarget

Article Title: A lesson for cancer research: placental microarray gene analysis in preeclampsia

doi:

Figure Lengend Snippet: Summary of microarray studies in preeclampsia

Article Snippet: Hoegh 2010 Denmark , 11 PE 18 ctrl , , , , Cs/vag. , Maternal side, center of cotyledons, stored differently, Pooled RNA. , Affymetrix HG-U133A Gene Chip , 12 up and 9 down in PE vs. ctrl. , Bradykinin B1 receptor, 14-3-3, INHBA, LEP , Placentation, oxidative stress, inflammation.

Techniques: Microarray, Sampling, Dissection, Expressing, Cell Function Assay

Journal: Oncogene

Article Title: Prediction of future metastasis and molecular characterization of head and neck squamous-cell carcinoma based on transcriptome and genome analysis by microarrays.

doi: 10.1038/onc.2008.251

Figure Lengend Snippet: Figure 2 RNA expression by seven genes relative to pathological differentiation. The box plots indicate the distribution of RNA levels measured by QRT–PCR in 134 tumour samples grouped by level of differentiation. The seven genes yielded significant P-values (Po0.01) based on Affymetrix data testing the different tumour differentiation classes. Colours correspond to the sample groups (green: well differentiated (n ¼ 40); orange: moderately differentiated (n ¼ 68); red: poorly differentiated (n ¼ 29)). The y axis gives the DCt values relative to the control genes (R18S and RPLP0). The bottom table shows the fold difference (FC) between the geometric mean values between the different classes and associated Wilcoxon P-value.

Article Snippet: Prediction analysis Initial selection was based on univariate and multivariate Cox analyses (survival R package v2.26) of Affymetrix gene chip variables using 81 samples, divided into three groups: training group S1 (20M and 20 NM samples), training group S2 (10M and 10 NM samples) and a validation group S3 (11M and 10 NM samples).

Techniques: RNA Expression, Quantitative RT-PCR, Control

Journal: Oncogene

Article Title: Prediction of future metastasis and molecular characterization of head and neck squamous-cell carcinoma based on transcriptome and genome analysis by microarrays.

doi: 10.1038/onc.2008.251

Figure Lengend Snippet: Figure 4 QRT–PCR validation of genes associated with metastasis. Transcripts (22) selected from the transcriptome array analysis (Affymetrix; Cox P-value o0.05) were quantitated by QRT–PCR analysis with 134 samples of M (n ¼ 46) and NM (n ¼ 88). Top: box plots (NM blue, M red) representing the distributions of the log2 value of the DCt values after power transformation. Bottom: the fold difference (FC) between the geometric mean values from M divided by NM samples and the p value calculated from the Cox univariate tests for each of the genes, using the entire population of 134 samples analysed by QRT–PCR.

Article Snippet: Prediction analysis Initial selection was based on univariate and multivariate Cox analyses (survival R package v2.26) of Affymetrix gene chip variables using 81 samples, divided into three groups: training group S1 (20M and 20 NM samples), training group S2 (10M and 10 NM samples) and a validation group S3 (11M and 10 NM samples).

Techniques: Quantitative RT-PCR, Biomarker Discovery, Transformation Assay