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  • 99
    Millipore microarrays
    Percentage increases in sIgE concentrations (≥0.35 IU/ml) to the different allergens. The results were obtained after analyses of serum samples from children ( green columns ) and adults ( red columns ) with the hydrogel <t>microarrays</t>
    Microarrays, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 344 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Thermo Fisher microarray probeset gi21622627 at
    Percentage increases in sIgE concentrations (≥0.35 IU/ml) to the different allergens. The results were obtained after analyses of serum samples from children ( green columns ) and adults ( red columns ) with the hydrogel <t>microarrays</t>
    Microarray Probeset Gi21622627 At, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Agilent technologies microarrays microarrays
    Gene expression profile of brain-infiltrating CD4 + and CD8 + TCCs. (A) TCC 4.1 (Tc2) and TCC 17.2. (Tc1) were stimulated and their expression profile analyzed by <t>microarrays.</t> Histogram values show differential expression of Tc1- and Tc2-associated genes measured as microarray fluorescence intensity. (B) TCC 17-1, TCC 21-1 and circulating memory CD4 + T cells were stimulated and their expression profile analyzed by microarrays. Heat map shows Th1-, Th2-, Th17- and Treg-associated genes differentially expressed in TCC 17-1 and TCC 21-1 compared with circulating memory CD4 + T cells. I and II are two independent expansions and stimulations of the same TCC. Blue are genes upregulated and yellow downregulated compared with expression in circulating memory CD4+ T cells. Values represent log2FC TCC – circulating memory CD4+ T cells.
    Microarrays Microarrays, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 86/100, based on 753 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore oligonucleotide microarray
    Selectivity and sensitivity of carB -based oligonucleotide <t>microarray.</t>
    Oligonucleotide Microarray, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    Genisphere microarrays
    Microarray analysis of DDC-regulated genes . Experimental outline of microarray studies to identify DDC downstream targets using LNCaP-DDC stable and control LNCaP-pDEST cells. In the presence of Dox ( grey triangle , + Dox) the tetracycline Tet repressor (tetR) is released from the TetO2 sequence in the promoter of the lentiviral construct containing the DDC gene. The dissociation of the tetR allows induction of transcription for the gene of interest. LNCaP-DDC and LNCaP-pDEST (vector control) cell lines were plated in medium containing 5% charcoal-stripped serum and incubated overnight. The next day, cells were treated for 48 hours under mock-induced (-Dox) and Dox-induced (+Dox) conditions, 24 h of which was in the presence or absence of 0.1 nM R1881. Total RNA samples were isolated from each condition, labeled and hybridized on the <t>microarrays.</t> The relative mRNA abundance of each gene was calculated as a ratio between hormone-treated (+R1881) and hormone-untreated (- R1881) samples. The comparison of the expression data obtained from LNCaP-DDC+Dox stable cells ( left ) with the expression data from the three LNCaP control cells ( right : LNCaP-DDC-Dox, LNCaP-pDEST- Dox, and LNCaP-pDEST+Dox) yielded the identification of genes that are androgen- and DDC-regulated.
    Microarrays, supplied by Genisphere, used in various techniques. Bioz Stars score: 87/100, based on 94 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Illumina Inc microarrays
    Identification of p53-regulated lncRNAs. ( A ) Isogenic p53-WT and p53-KO HCT116 cells were untreated or treated with Nutlin-3 for 8 hr and immunoblotting was performed for p53 and the loading control GAPDH. ( B ) Heat map is shown for the differentially expressed mRNAs and lncRNAs identified by <t>microarrays</t> performed in duplicate from HCT116, SW48 and RKO cells untreated or treated with Nutlin-3 for 8 hr. Upregulated genes are shown in red and downregulated genes in green. PINCR ( RP3-326I13.1 ) is shown in the red box. ( C ) Venn diagram showing the overlap between the transcriptomes upregulated ≥1.5-fold after Nutlin-3 treatment of HCT116, SW48 and RKO cells. DOI: http://dx.doi.org/10.7554/eLife.23244.004 10.7554/eLife.23244.005 p53 immunoblot for Figure 1—figure supplement 1A . DOI: http://dx.doi.org/10.7554/eLife.23244.005
    Microarrays, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1711 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher microarrays
    Comparison of the relative expression of the Wnt pathway inhibitors in healthy nonsmokers (n = 47), healthy smokers (n = 58), and smokers with COPD (n = 22). Analysis was carried out with HG-U133 plus 2.0 <t>microarrays.</t> Each bar represents mean expression with standard error; p values are represented in brackets above the bars.
    Microarrays, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 11812 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Bioarray microarrays
    Comparison of the relative expression of the Wnt pathway inhibitors in healthy nonsmokers (n = 47), healthy smokers (n = 58), and smokers with COPD (n = 22). Analysis was carried out with HG-U133 plus 2.0 <t>microarrays.</t> Each bar represents mean expression with standard error; p values are represented in brackets above the bars.
    Microarrays, supplied by Bioarray, used in various techniques. Bioz Stars score: 92/100, based on 56 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher microarray hg u133a microarray
    Comparison of the relative expression of the Wnt pathway inhibitors in healthy nonsmokers (n = 47), healthy smokers (n = 58), and smokers with COPD (n = 22). Analysis was carried out with HG-U133 plus 2.0 <t>microarrays.</t> Each bar represents mean expression with standard error; p values are represented in brackets above the bars.
    Microarray Hg U133a Microarray, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Biodiscovery LLC microarray hybridizations microarray slides
    Comparison of the relative expression of the Wnt pathway inhibitors in healthy nonsmokers (n = 47), healthy smokers (n = 58), and smokers with COPD (n = 22). Analysis was carried out with HG-U133 plus 2.0 <t>microarrays.</t> Each bar represents mean expression with standard error; p values are represented in brackets above the bars.
    Microarray Hybridizations Microarray Slides, supplied by Biodiscovery LLC, used in various techniques. Bioz Stars score: 86/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Alere microarrays
    Comparison of the relative expression of the Wnt pathway inhibitors in healthy nonsmokers (n = 47), healthy smokers (n = 58), and smokers with COPD (n = 22). Analysis was carried out with HG-U133 plus 2.0 <t>microarrays.</t> Each bar represents mean expression with standard error; p values are represented in brackets above the bars.
    Microarrays, supplied by Alere, used in various techniques. Bioz Stars score: 92/100, based on 69 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Alta Bioscience microarrays
    Comparison of the relative expression of the Wnt pathway inhibitors in healthy nonsmokers (n = 47), healthy smokers (n = 58), and smokers with COPD (n = 22). Analysis was carried out with HG-U133 plus 2.0 <t>microarrays.</t> Each bar represents mean expression with standard error; p values are represented in brackets above the bars.
    Microarrays, supplied by Alta Bioscience, used in various techniques. Bioz Stars score: 86/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Arraystar microarrays
    Transcriptome-wide identification of HuR-associated circRNAs. (A,B) Schematic of the strategy used to identify globally HuR-interacting circRNAs in HeLa cells (A). Following cell lysis, RIP analysis was carried out using anti-HuR or control IgG antibodies; the presence of HuR in the IP samples was assessed by Western blot analysis [(B); HC, heavy IgG chain]. Total RNA was isolated and digested with RNase R, and circRNAs present in the sample were identified using circRNA <t>microarrays</t> (Arraystar). (C) Partial list of circRNAs highly enriched in HuR IP relative to IgG IP as identified in microarrays (n = 3).
    Microarrays, supplied by Arraystar, used in various techniques. Bioz Stars score: 92/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche microarrays
    ) was hybridized to tiling <t>microarrays</t> together with in vitro ) have been excluded because nucleosome spacing is different in these regions. Dotted lines at multiples of the estimated nucleosome repeat length (NRL) indicate positions of peaks and valleys corresponding to nucleosomes and linker DNA in white (black) and H3.3 (grey) knockdown cells.
    Microarrays, supplied by Roche, used in various techniques. Bioz Stars score: 93/100, based on 742 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    BlueGnome Limited microarrays
    S. mansoni gDNA has superior hybridization characteristics compared to S. mansoni cDNA. The use of S. mansoni gDNA as a common reference reveals higher median intensity values and narrower overall intensity distributions than a complex S. mansoni cDNA reference. Box-plots display signal intensities for the AF-555 channel for S. japonicum , S. mansoni , M. musculus gDNA and complex reference S. mansoni cDNA pool (as described in Methods ). Boxes represent three independent experiments for mouse gDNA, S. mansoni gDNA and S. mansoni cDNA pool, respectively. S. japonicum gDNA is represented by a single experiment. All negative control microarray signals were removed before analysis, <t>microarrays</t> were filtered for manually excluded spots and each experiment was subsequently filtered to contain the same number of spots (n = 32,746). Statistical significance was defined using a Student's t-test between three independently replicated experiments. Horizontal lines represent median oligonucleotide intensity, boxes display oligonucleotide elements 25% above and below the median value and whiskers show oligonucleotide elements within 1.5 deviations of the median. Outlier oligonucleotide intensity values (beyond 1.5 deviations) are illustrated as individual spots.
    Microarrays, supplied by BlueGnome Limited, used in various techniques. Bioz Stars score: 86/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    CombiMatrix microarrays
    S. mansoni gDNA has superior hybridization characteristics compared to S. mansoni cDNA. The use of S. mansoni gDNA as a common reference reveals higher median intensity values and narrower overall intensity distributions than a complex S. mansoni cDNA reference. Box-plots display signal intensities for the AF-555 channel for S. japonicum , S. mansoni , M. musculus gDNA and complex reference S. mansoni cDNA pool (as described in Methods ). Boxes represent three independent experiments for mouse gDNA, S. mansoni gDNA and S. mansoni cDNA pool, respectively. S. japonicum gDNA is represented by a single experiment. All negative control microarray signals were removed before analysis, <t>microarrays</t> were filtered for manually excluded spots and each experiment was subsequently filtered to contain the same number of spots (n = 32,746). Statistical significance was defined using a Student's t-test between three independently replicated experiments. Horizontal lines represent median oligonucleotide intensity, boxes display oligonucleotide elements 25% above and below the median value and whiskers show oligonucleotide elements within 1.5 deviations of the median. Outlier oligonucleotide intensity values (beyond 1.5 deviations) are illustrated as individual spots.
    Microarrays, supplied by CombiMatrix, used in various techniques. Bioz Stars score: 93/100, based on 109 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Ocimum Biosolutions microarrays
    S. mansoni gDNA has superior hybridization characteristics compared to S. mansoni cDNA. The use of S. mansoni gDNA as a common reference reveals higher median intensity values and narrower overall intensity distributions than a complex S. mansoni cDNA reference. Box-plots display signal intensities for the AF-555 channel for S. japonicum , S. mansoni , M. musculus gDNA and complex reference S. mansoni cDNA pool (as described in Methods ). Boxes represent three independent experiments for mouse gDNA, S. mansoni gDNA and S. mansoni cDNA pool, respectively. S. japonicum gDNA is represented by a single experiment. All negative control microarray signals were removed before analysis, <t>microarrays</t> were filtered for manually excluded spots and each experiment was subsequently filtered to contain the same number of spots (n = 32,746). Statistical significance was defined using a Student's t-test between three independently replicated experiments. Horizontal lines represent median oligonucleotide intensity, boxes display oligonucleotide elements 25% above and below the median value and whiskers show oligonucleotide elements within 1.5 deviations of the median. Outlier oligonucleotide intensity values (beyond 1.5 deviations) are illustrated as individual spots.
    Microarrays, supplied by Ocimum Biosolutions, used in various techniques. Bioz Stars score: 87/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    PerkinElmer microarrays
    S. mansoni gDNA has superior hybridization characteristics compared to S. mansoni cDNA. The use of S. mansoni gDNA as a common reference reveals higher median intensity values and narrower overall intensity distributions than a complex S. mansoni cDNA reference. Box-plots display signal intensities for the AF-555 channel for S. japonicum , S. mansoni , M. musculus gDNA and complex reference S. mansoni cDNA pool (as described in Methods ). Boxes represent three independent experiments for mouse gDNA, S. mansoni gDNA and S. mansoni cDNA pool, respectively. S. japonicum gDNA is represented by a single experiment. All negative control microarray signals were removed before analysis, <t>microarrays</t> were filtered for manually excluded spots and each experiment was subsequently filtered to contain the same number of spots (n = 32,746). Statistical significance was defined using a Student's t-test between three independently replicated experiments. Horizontal lines represent median oligonucleotide intensity, boxes display oligonucleotide elements 25% above and below the median value and whiskers show oligonucleotide elements within 1.5 deviations of the median. Outlier oligonucleotide intensity values (beyond 1.5 deviations) are illustrated as individual spots.
    Microarrays, supplied by PerkinElmer, used in various techniques. Bioz Stars score: 96/100, based on 724 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    Incyte microarrays
    S. mansoni gDNA has superior hybridization characteristics compared to S. mansoni cDNA. The use of S. mansoni gDNA as a common reference reveals higher median intensity values and narrower overall intensity distributions than a complex S. mansoni cDNA reference. Box-plots display signal intensities for the AF-555 channel for S. japonicum , S. mansoni , M. musculus gDNA and complex reference S. mansoni cDNA pool (as described in Methods ). Boxes represent three independent experiments for mouse gDNA, S. mansoni gDNA and S. mansoni cDNA pool, respectively. S. japonicum gDNA is represented by a single experiment. All negative control microarray signals were removed before analysis, <t>microarrays</t> were filtered for manually excluded spots and each experiment was subsequently filtered to contain the same number of spots (n = 32,746). Statistical significance was defined using a Student's t-test between three independently replicated experiments. Horizontal lines represent median oligonucleotide intensity, boxes display oligonucleotide elements 25% above and below the median value and whiskers show oligonucleotide elements within 1.5 deviations of the median. Outlier oligonucleotide intensity values (beyond 1.5 deviations) are illustrated as individual spots.
    Microarrays, supplied by Incyte, used in various techniques. Bioz Stars score: 87/100, based on 38 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    NanoString Technologies Inc microarrays
    S. mansoni gDNA has superior hybridization characteristics compared to S. mansoni cDNA. The use of S. mansoni gDNA as a common reference reveals higher median intensity values and narrower overall intensity distributions than a complex S. mansoni cDNA reference. Box-plots display signal intensities for the AF-555 channel for S. japonicum , S. mansoni , M. musculus gDNA and complex reference S. mansoni cDNA pool (as described in Methods ). Boxes represent three independent experiments for mouse gDNA, S. mansoni gDNA and S. mansoni cDNA pool, respectively. S. japonicum gDNA is represented by a single experiment. All negative control microarray signals were removed before analysis, <t>microarrays</t> were filtered for manually excluded spots and each experiment was subsequently filtered to contain the same number of spots (n = 32,746). Statistical significance was defined using a Student's t-test between three independently replicated experiments. Horizontal lines represent median oligonucleotide intensity, boxes display oligonucleotide elements 25% above and below the median value and whiskers show oligonucleotide elements within 1.5 deviations of the median. Outlier oligonucleotide intensity values (beyond 1.5 deviations) are illustrated as individual spots.
    Microarrays, supplied by NanoString Technologies Inc, used in various techniques. Bioz Stars score: 96/100, based on 54 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    AutoGenomics microarrays
    S. mansoni gDNA has superior hybridization characteristics compared to S. mansoni cDNA. The use of S. mansoni gDNA as a common reference reveals higher median intensity values and narrower overall intensity distributions than a complex S. mansoni cDNA reference. Box-plots display signal intensities for the AF-555 channel for S. japonicum , S. mansoni , M. musculus gDNA and complex reference S. mansoni cDNA pool (as described in Methods ). Boxes represent three independent experiments for mouse gDNA, S. mansoni gDNA and S. mansoni cDNA pool, respectively. S. japonicum gDNA is represented by a single experiment. All negative control microarray signals were removed before analysis, <t>microarrays</t> were filtered for manually excluded spots and each experiment was subsequently filtered to contain the same number of spots (n = 32,746). Statistical significance was defined using a Student's t-test between three independently replicated experiments. Horizontal lines represent median oligonucleotide intensity, boxes display oligonucleotide elements 25% above and below the median value and whiskers show oligonucleotide elements within 1.5 deviations of the median. Outlier oligonucleotide intensity values (beyond 1.5 deviations) are illustrated as individual spots.
    Microarrays, supplied by AutoGenomics, used in various techniques. Bioz Stars score: 94/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Kaneka Corp microarrays
    S. mansoni gDNA has superior hybridization characteristics compared to S. mansoni cDNA. The use of S. mansoni gDNA as a common reference reveals higher median intensity values and narrower overall intensity distributions than a complex S. mansoni cDNA reference. Box-plots display signal intensities for the AF-555 channel for S. japonicum , S. mansoni , M. musculus gDNA and complex reference S. mansoni cDNA pool (as described in Methods ). Boxes represent three independent experiments for mouse gDNA, S. mansoni gDNA and S. mansoni cDNA pool, respectively. S. japonicum gDNA is represented by a single experiment. All negative control microarray signals were removed before analysis, <t>microarrays</t> were filtered for manually excluded spots and each experiment was subsequently filtered to contain the same number of spots (n = 32,746). Statistical significance was defined using a Student's t-test between three independently replicated experiments. Horizontal lines represent median oligonucleotide intensity, boxes display oligonucleotide elements 25% above and below the median value and whiskers show oligonucleotide elements within 1.5 deviations of the median. Outlier oligonucleotide intensity values (beyond 1.5 deviations) are illustrated as individual spots.
    Microarrays, supplied by Kaneka Corp, used in various techniques. Bioz Stars score: 88/100, based on 36 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Corning Life Sciences microarrays
    Outline of the experimental approach used to identify 17 novel genes in F. diplosiphon that are responsive to changes in light color. Steps involved in the construction and analysis of genomic DNA <t>microarrays,</t> subarrays, Northern blots, and slot blots are shown.
    Microarrays, supplied by Corning Life Sciences, used in various techniques. Bioz Stars score: 90/100, based on 247 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    US Biomax microarrays
    Outline of the experimental approach used to identify 17 novel genes in F. diplosiphon that are responsive to changes in light color. Steps involved in the construction and analysis of genomic DNA <t>microarrays,</t> subarrays, Northern blots, and slot blots are shown.
    Microarrays, supplied by US Biomax, used in various techniques. Bioz Stars score: 86/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    LC Sciences microarrays
    Outline of the experimental approach used to identify 17 novel genes in F. diplosiphon that are responsive to changes in light color. Steps involved in the construction and analysis of genomic DNA <t>microarrays,</t> subarrays, Northern blots, and slot blots are shown.
    Microarrays, supplied by LC Sciences, used in various techniques. Bioz Stars score: 94/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    MOgene microarrays
    Outline of the experimental approach used to identify 17 novel genes in F. diplosiphon that are responsive to changes in light color. Steps involved in the construction and analysis of genomic DNA <t>microarrays,</t> subarrays, Northern blots, and slot blots are shown.
    Microarrays, supplied by MOgene, used in various techniques. Bioz Stars score: 93/100, based on 59 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher microarray data microarray data
    Outline of the experimental approach used to identify 17 novel genes in F. diplosiphon that are responsive to changes in light color. Steps involved in the construction and analysis of genomic DNA <t>microarrays,</t> subarrays, Northern blots, and slot blots are shown.
    Microarray Data Microarray Data, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore microarray hybridization
    Altered epigenetic markers of the alpha-lactalbumin ( Lalba ) gene observed in BPA-exposed mammary glands. A. BPA-induced DNA demethylation near the Lalba promoter. p-values of the DNA methylation calculated from the <t>microarray-based</t> DNA methylation analysis are indicated. The PCR amplicon position for the ChIP-seq assay of H3K4me3 is shown as a red bar. B. ChIP assay of H3K4me3 at the Lalba transcription initiation site in the PND4 mammary glands. C. Quantitation following histone immunoprecipitation indicates enrichment of the Lalba promoter for the histone H3K4.
    Microarray Hybridization, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 110 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    Agilent technologies microarray description a porcine microarray gpl16524
    Altered epigenetic markers of the alpha-lactalbumin ( Lalba ) gene observed in BPA-exposed mammary glands. A. BPA-induced DNA demethylation near the Lalba promoter. p-values of the DNA methylation calculated from the <t>microarray-based</t> DNA methylation analysis are indicated. The PCR amplicon position for the ChIP-seq assay of H3K4me3 is shown as a red bar. B. ChIP assay of H3K4me3 at the Lalba transcription initiation site in the PND4 mammary glands. C. Quantitation following histone immunoprecipitation indicates enrichment of the Lalba promoter for the histone H3K4.
    Microarray Description A Porcine Microarray Gpl16524, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 87/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher gscs microarray data microarray data
    Altered epigenetic markers of the alpha-lactalbumin ( Lalba ) gene observed in BPA-exposed mammary glands. A. BPA-induced DNA demethylation near the Lalba promoter. p-values of the DNA methylation calculated from the <t>microarray-based</t> DNA methylation analysis are indicated. The PCR amplicon position for the ChIP-seq assay of H3K4me3 is shown as a red bar. B. ChIP assay of H3K4me3 at the Lalba transcription initiation site in the PND4 mammary glands. C. Quantitation following histone immunoprecipitation indicates enrichment of the Lalba promoter for the histone H3K4.
    Gscs Microarray Data Microarray Data, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 90 stars, based on 2 article reviews
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    Image Search Results


    Percentage increases in sIgE concentrations (≥0.35 IU/ml) to the different allergens. The results were obtained after analyses of serum samples from children ( green columns ) and adults ( red columns ) with the hydrogel microarrays

    Journal: Clinical Proteomics

    Article Title: Development of a microarray-based method for allergen-specific IgE and IgG4 detection

    doi: 10.1186/s12014-016-9136-7

    Figure Lengend Snippet: Percentage increases in sIgE concentrations (≥0.35 IU/ml) to the different allergens. The results were obtained after analyses of serum samples from children ( green columns ) and adults ( red columns ) with the hydrogel microarrays

    Article Snippet: Analysis of sIgE and sIgG4 on the microarrays Each microarray was incubated with sixty-five microliters of blood serum at 37 °C for 20 h. After washing in PBST (PBS, 0.1% Tween-20 (Sigma, USA)) for 20 min, 50 µl of developing solution containing anti-IgE-Cy5 and/or anti-IgG4-Cy3 (working concentrations of 2.5 and 1.5 µg/ml, respectively) was applied to the microarray, and the microarray was incubated at 37 °C for 1 h in the dark.

    Techniques:

    Gene expression profile of brain-infiltrating CD4 + and CD8 + TCCs. (A) TCC 4.1 (Tc2) and TCC 17.2. (Tc1) were stimulated and their expression profile analyzed by microarrays. Histogram values show differential expression of Tc1- and Tc2-associated genes measured as microarray fluorescence intensity. (B) TCC 17-1, TCC 21-1 and circulating memory CD4 + T cells were stimulated and their expression profile analyzed by microarrays. Heat map shows Th1-, Th2-, Th17- and Treg-associated genes differentially expressed in TCC 17-1 and TCC 21-1 compared with circulating memory CD4 + T cells. I and II are two independent expansions and stimulations of the same TCC. Blue are genes upregulated and yellow downregulated compared with expression in circulating memory CD4+ T cells. Values represent log2FC TCC – circulating memory CD4+ T cells.

    Journal: Annals of Clinical and Translational Neurology

    Article Title: Central role of Th2/Tc2 lymphocytes in pattern II multiple sclerosis lesions

    doi: 10.1002/acn3.218

    Figure Lengend Snippet: Gene expression profile of brain-infiltrating CD4 + and CD8 + TCCs. (A) TCC 4.1 (Tc2) and TCC 17.2. (Tc1) were stimulated and their expression profile analyzed by microarrays. Histogram values show differential expression of Tc1- and Tc2-associated genes measured as microarray fluorescence intensity. (B) TCC 17-1, TCC 21-1 and circulating memory CD4 + T cells were stimulated and their expression profile analyzed by microarrays. Heat map shows Th1-, Th2-, Th17- and Treg-associated genes differentially expressed in TCC 17-1 and TCC 21-1 compared with circulating memory CD4 + T cells. I and II are two independent expansions and stimulations of the same TCC. Blue are genes upregulated and yellow downregulated compared with expression in circulating memory CD4+ T cells. Values represent log2FC TCC – circulating memory CD4+ T cells.

    Article Snippet: Microarrays Microarrays were done using the “Low RNA Input linear Amplification Kit Plus, One Color” protocol (Cat. No.: 5188-5339, 2007; Agilent Technologies, Inc., Santa Clara, CA) and the Agilent RNA Spike-In Kit for One color (Agilent Technologies, Inc. 2007; Cat. No.: 5188-5282) following the manufacturer's standard protocol.

    Techniques: Expressing, Microarray, Fluorescence

    Microarrays had consistent data quality across groups. A, We verified that in our 2-color hybridizations, most of the inter-group variation in gene expression was due to variability of the sample channel (red) but not the reference channel (green). We computed the standard deviation, across the 20 arrays, of the raw signal intensity of the sample red channel (black) and the reference green channel (light grey), respectively, at three percentiles of the signal distribution. For all tested percentiles, the standard deviation from the sample channel was clearly much higher than that from the reference channel (F-test on variances, p

    Journal: PLoS ONE

    Article Title: Gene Expression Changes in the Motor Cortex Mediating Motor Skill Learning

    doi: 10.1371/journal.pone.0061496

    Figure Lengend Snippet: Microarrays had consistent data quality across groups. A, We verified that in our 2-color hybridizations, most of the inter-group variation in gene expression was due to variability of the sample channel (red) but not the reference channel (green). We computed the standard deviation, across the 20 arrays, of the raw signal intensity of the sample red channel (black) and the reference green channel (light grey), respectively, at three percentiles of the signal distribution. For all tested percentiles, the standard deviation from the sample channel was clearly much higher than that from the reference channel (F-test on variances, p

    Article Snippet: RNA Extraction and Microarray Processing In our microarray experiment, the motor cortical transcriptome of each animal (Reach or Sham ) was hybridized to a single 2-color gene array; thus, a total of 20 microarrays (Agilent whole rat genome; G4131F; design ID: 01479; 41,012 unique biological probes) were employed.

    Techniques: Expressing, Standard Deviation

    Gene expression in maize leaf. As assayed by Agilent microarray analysis, 10,037 transcripts were identified as diurnally cycling with a period near 24 hours via the GeneTS method. A) A heat map showing normalized gene expression patterns of significant transcripts. Each transcript is normalized to the median of that transcript's signal intensity. Color scale runs from 0.25 (blue) to 4 (yellow). B) Phase diagram of significant cycling transcripts, as determined by greatest mean expression. Time points immediately following light/dark transitions are enriched for peak expression.

    Journal: PLoS ONE

    Article Title: Maize Global Transcriptomics Reveals Pervasive Leaf Diurnal Rhythms but Rhythms in Developing Ears Are Largely Limited to the Core Oscillator

    doi: 10.1371/journal.pone.0012887

    Figure Lengend Snippet: Gene expression in maize leaf. As assayed by Agilent microarray analysis, 10,037 transcripts were identified as diurnally cycling with a period near 24 hours via the GeneTS method. A) A heat map showing normalized gene expression patterns of significant transcripts. Each transcript is normalized to the median of that transcript's signal intensity. Color scale runs from 0.25 (blue) to 4 (yellow). B) Phase diagram of significant cycling transcripts, as determined by greatest mean expression. Time points immediately following light/dark transitions are enriched for peak expression.

    Article Snippet: This gene encodes a protein with 47% identity and 53% similarity to Arabidopsis CHE; however, on the Agilent microarray the maize CHE mRNA does not display a diurnal pattern.

    Techniques: Expressing, Microarray

    Gene expression in maize developing ears. As assayed by Agilent microarray analysis, 149 transcripts were identified as cycling with a period near 24 hours via the GeneTS method. A) A heat map showing normalized gene expression patterns of significant transcripts. Each transcript is normalized to the median of that transcript's signal intensity. Color scale runs from 0.25 (blue) to 4 (yellow). B) Phase diagram of significant cycling transcripts, as determined by greatest mean expression. Despite low numbers of cycling transcripts, there appears to be enrichment for early evening peak expression.

    Journal: PLoS ONE

    Article Title: Maize Global Transcriptomics Reveals Pervasive Leaf Diurnal Rhythms but Rhythms in Developing Ears Are Largely Limited to the Core Oscillator

    doi: 10.1371/journal.pone.0012887

    Figure Lengend Snippet: Gene expression in maize developing ears. As assayed by Agilent microarray analysis, 149 transcripts were identified as cycling with a period near 24 hours via the GeneTS method. A) A heat map showing normalized gene expression patterns of significant transcripts. Each transcript is normalized to the median of that transcript's signal intensity. Color scale runs from 0.25 (blue) to 4 (yellow). B) Phase diagram of significant cycling transcripts, as determined by greatest mean expression. Despite low numbers of cycling transcripts, there appears to be enrichment for early evening peak expression.

    Article Snippet: This gene encodes a protein with 47% identity and 53% similarity to Arabidopsis CHE; however, on the Agilent microarray the maize CHE mRNA does not display a diurnal pattern.

    Techniques: Expressing, Microarray

    Aiolos and Blimp-1 collaboratively regulate gene expression and maintain the survival of MM cells. ( a ) Heatmap of microarray data from the H929 line transduced with shCtrl, shAiolos or shBlimp-1 for 4 days. The changes in expression for each gene were calculated as the ratio of expression in shAiolos- or shBlimp-1-transduced cells versus shCtrl-transduced cells. Microarray experiments were performed in duplicate. Each row represents a significantly induced (red) or repressed (green) gene following knockdown of Aiolos or Blimp-1. ( b ) Pie charts show the results of GO analysis of Blimp-1-dependent genes (left panel) or Aiolos-dependent genes (right panel) in H929 cells. ( c ) RT-QPCR analysis with samples from ( a ) validated the expression of apoptosis-related genes in shRNA-expressing cells. ( d ) Chromatin from H929 cells was subjected to the ChIP assay using anti-Blimp-1 or anti-Aiolos, followed by QPCR to quantify the binding of Blimp-1 or Aiolos to the indicated genes. ( e ) Immunoblots show the knockdown efficiency of shBlimp-1 and shAiolos in three MM cell lines expressing indicated shRNA for 3 days. ( f ) Flow cytometric analysis of annexin V staining shows the increased apoptosis in MM cells expressing shAiolos or shBlimp-1 for 3 days. Data in c and d represent the mean±S.E.M. ( n =3). * P

    Journal: Cell Death and Differentiation

    Article Title: Aiolos collaborates with Blimp-1 to regulate the survival of multiple myeloma cells

    doi: 10.1038/cdd.2015.167

    Figure Lengend Snippet: Aiolos and Blimp-1 collaboratively regulate gene expression and maintain the survival of MM cells. ( a ) Heatmap of microarray data from the H929 line transduced with shCtrl, shAiolos or shBlimp-1 for 4 days. The changes in expression for each gene were calculated as the ratio of expression in shAiolos- or shBlimp-1-transduced cells versus shCtrl-transduced cells. Microarray experiments were performed in duplicate. Each row represents a significantly induced (red) or repressed (green) gene following knockdown of Aiolos or Blimp-1. ( b ) Pie charts show the results of GO analysis of Blimp-1-dependent genes (left panel) or Aiolos-dependent genes (right panel) in H929 cells. ( c ) RT-QPCR analysis with samples from ( a ) validated the expression of apoptosis-related genes in shRNA-expressing cells. ( d ) Chromatin from H929 cells was subjected to the ChIP assay using anti-Blimp-1 or anti-Aiolos, followed by QPCR to quantify the binding of Blimp-1 or Aiolos to the indicated genes. ( e ) Immunoblots show the knockdown efficiency of shBlimp-1 and shAiolos in three MM cell lines expressing indicated shRNA for 3 days. ( f ) Flow cytometric analysis of annexin V staining shows the increased apoptosis in MM cells expressing shAiolos or shBlimp-1 for 3 days. Data in c and d represent the mean±S.E.M. ( n =3). * P

    Article Snippet: The amplified DNA was labeled and hybridized to microarray chips (Agilent Technologies, Santa Clara, CA, USA), with subsequent analysis by the WELGENE Company (Taipei, Taiwan).

    Techniques: Expressing, Microarray, Transduction, Quantitative RT-PCR, shRNA, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Binding Assay, Western Blot, Flow Cytometry, Staining

    Volcano plot of microarray analysis. In this microarray a total of 22,863 probes were analyzed. On the y-axis the negative log10 of the adjusted p -value and on the x-axis the log2 of the fold-change is plotted. Each probe is represented as a dot. Low p -values (highly significant) are localized at the top of the plot. Probes that are expressed higher in females have a negative log2 fold-change appearing at the left side and probes that are expressed higher in males have a positive log2 fold-change appearing at the right side. The horizontal red line denotes the threshold for p = 0.05. The vertical red lines denote the two-fold thresholds.

    Journal: PLoS ONE

    Article Title: Male-Dominant Activation of Rat Renal Organic Anion Transporter 1 (Oat1) and 3 (Oat3) Expression by Transcription Factor BCL6

    doi: 10.1371/journal.pone.0035556

    Figure Lengend Snippet: Volcano plot of microarray analysis. In this microarray a total of 22,863 probes were analyzed. On the y-axis the negative log10 of the adjusted p -value and on the x-axis the log2 of the fold-change is plotted. Each probe is represented as a dot. Low p -values (highly significant) are localized at the top of the plot. Probes that are expressed higher in females have a negative log2 fold-change appearing at the left side and probes that are expressed higher in males have a positive log2 fold-change appearing at the right side. The horizontal red line denotes the threshold for p = 0.05. The vertical red lines denote the two-fold thresholds.

    Article Snippet: Sex-dependent gene expression profiling The gene expression profiles of cortical kidney slices from the four male and four female rats used previously, were analyzed using the SurePrint G3 Rat GE 8×60K Microarray Kit from Agilent Technologies.

    Techniques: Microarray

    Verification of microarray results using TaqMan® real-time PCR. Gene expressions were verified by TaqMan® real-time PCR in total RNA isolated from four male and four female cortical kidney slices. Levels of all genes were determined using 2 −ΔΔCt method, at which β-actin was the reference gene. ΔΔCt values were calculated as ΔCt male - ΔCt female. n male = 4; n female = 4.

    Journal: PLoS ONE

    Article Title: Male-Dominant Activation of Rat Renal Organic Anion Transporter 1 (Oat1) and 3 (Oat3) Expression by Transcription Factor BCL6

    doi: 10.1371/journal.pone.0035556

    Figure Lengend Snippet: Verification of microarray results using TaqMan® real-time PCR. Gene expressions were verified by TaqMan® real-time PCR in total RNA isolated from four male and four female cortical kidney slices. Levels of all genes were determined using 2 −ΔΔCt method, at which β-actin was the reference gene. ΔΔCt values were calculated as ΔCt male - ΔCt female. n male = 4; n female = 4.

    Article Snippet: Sex-dependent gene expression profiling The gene expression profiles of cortical kidney slices from the four male and four female rats used previously, were analyzed using the SurePrint G3 Rat GE 8×60K Microarray Kit from Agilent Technologies.

    Techniques: Microarray, Real-time Polymerase Chain Reaction, Isolation

    Expression of Ccl8 and Apod with aging, senescence and cell type. ( A,B ) Confirmation of stromal age-related changes in gene expression by qRT-PCR. RNAs were reverse transcribed and amplified using qRT-PCR with primers specific for Ccl8 and Apod . RNAs analyzed: microdissected glandular-adjacent stroma (STR) and epithelium (EPI) from dorsal (n = 4) and anterior (n = 4) prostate lobes from C57BL/6 young (n = 12) and old (n = 12) mice used in microarray analyses. White blood cells (WBC) were isolated from young and old C57BL/6 mice (n = 6). Note the higher expression of Ccl8 and Apod in the microdissected old stroma (Old STR) compared to young stroma (young STR). Also notice the low abundance in transcript levels of these two genes in microdissected young and old epithelium (Young EPI, Old EPI, respectively) and in white-blood cells (WBC). ( C ) Human pre-senescent and senescent prostate PSC27 fibroblasts. Pre-SEN: pre-senescent cells; SEN (ASH) cells induced to senesce by H 2 O 2 exposure; SEN (Bleo) cells induced to senesce by bleomycin exposure; SEN (Rad) cells induced to senesce by radiation exposure; RPL13 transcript expression levels were used to normalize the human qRT-PCR data.

    Journal: PLoS ONE

    Article Title: The Effects of Aging on the Molecular and Cellular Composition of the Prostate Microenvironment

    doi: 10.1371/journal.pone.0012501

    Figure Lengend Snippet: Expression of Ccl8 and Apod with aging, senescence and cell type. ( A,B ) Confirmation of stromal age-related changes in gene expression by qRT-PCR. RNAs were reverse transcribed and amplified using qRT-PCR with primers specific for Ccl8 and Apod . RNAs analyzed: microdissected glandular-adjacent stroma (STR) and epithelium (EPI) from dorsal (n = 4) and anterior (n = 4) prostate lobes from C57BL/6 young (n = 12) and old (n = 12) mice used in microarray analyses. White blood cells (WBC) were isolated from young and old C57BL/6 mice (n = 6). Note the higher expression of Ccl8 and Apod in the microdissected old stroma (Old STR) compared to young stroma (young STR). Also notice the low abundance in transcript levels of these two genes in microdissected young and old epithelium (Young EPI, Old EPI, respectively) and in white-blood cells (WBC). ( C ) Human pre-senescent and senescent prostate PSC27 fibroblasts. Pre-SEN: pre-senescent cells; SEN (ASH) cells induced to senesce by H 2 O 2 exposure; SEN (Bleo) cells induced to senesce by bleomycin exposure; SEN (Rad) cells induced to senesce by radiation exposure; RPL13 transcript expression levels were used to normalize the human qRT-PCR data.

    Article Snippet: Heat map of differentially expressed genes (p < 0.05) from microdissected glandular-adjacent stroma, using an independent set of 4 month-old (n = 12) and 24 month-old (n = 12) C57BL/6 mice and a microarray platform comprised of oligonucleotides complementary to ∼40,000 genes (Agilent).

    Techniques: Expressing, Quantitative RT-PCR, Amplification, Mouse Assay, Microarray, Isolation

    Age and cell type-specific transcript profiles in the mouse prostate. A ) Principal Component Analysis (PCA) for microdissected dorsal prostate stroma and epithelium from young and old animals. PCA discriminates epithelial and stromal samples. EO : old epithelium; EY : young epithelium; SO : old stroma; SY : young stroma. B ) Transcript abundance levels (Log2 Ratios) obtained from microarray-based measurements for genes known to exhibit preferentially expression in stromal or epithelial cells. Red indicates increased expression; green indicates decreased expression. C ) Heat map of age-associated transcripts in the prostate stroma (p

    Journal: PLoS ONE

    Article Title: The Effects of Aging on the Molecular and Cellular Composition of the Prostate Microenvironment

    doi: 10.1371/journal.pone.0012501

    Figure Lengend Snippet: Age and cell type-specific transcript profiles in the mouse prostate. A ) Principal Component Analysis (PCA) for microdissected dorsal prostate stroma and epithelium from young and old animals. PCA discriminates epithelial and stromal samples. EO : old epithelium; EY : young epithelium; SO : old stroma; SY : young stroma. B ) Transcript abundance levels (Log2 Ratios) obtained from microarray-based measurements for genes known to exhibit preferentially expression in stromal or epithelial cells. Red indicates increased expression; green indicates decreased expression. C ) Heat map of age-associated transcripts in the prostate stroma (p

    Article Snippet: Heat map of differentially expressed genes (p < 0.05) from microdissected glandular-adjacent stroma, using an independent set of 4 month-old (n = 12) and 24 month-old (n = 12) C57BL/6 mice and a microarray platform comprised of oligonucleotides complementary to ∼40,000 genes (Agilent).

    Techniques: Microarray, Expressing

    Identification of robust candidate genes allowing discrimination of different radiation qualities. (A, B) DNAJC1 and PRTFDC1 6 h after withdrawal of 123 IUdR versus 24 h after γ-irradiation; (C) PPP1R14C 6 h after withdrawal of 123 IUdR versus 6 h after γ-irradiation; (D) KLF10 24 h after γ-irradiation versus 24 h after α-irradiation; (E) TNFAIP8L1 6 h after withdrawal of 123 IUdR versus 6 h after γ- and α-irradiation. Solid bars show the data of the quantitative real-time PCR in comparison with the microarray data (white bars with dashed lines). The error bars represent the standard deviation of the mean ( n = 3, * P

    Journal: Journal of Radiation Research

    Article Title: Comparative gene expression analysis after exposure to 123I-iododeoxyuridine, γ- and α-radiation—potential biomarkers for the discrimination of radiation qualities

    doi: 10.1093/jrr/rry038

    Figure Lengend Snippet: Identification of robust candidate genes allowing discrimination of different radiation qualities. (A, B) DNAJC1 and PRTFDC1 6 h after withdrawal of 123 IUdR versus 24 h after γ-irradiation; (C) PPP1R14C 6 h after withdrawal of 123 IUdR versus 6 h after γ-irradiation; (D) KLF10 24 h after γ-irradiation versus 24 h after α-irradiation; (E) TNFAIP8L1 6 h after withdrawal of 123 IUdR versus 6 h after γ- and α-irradiation. Solid bars show the data of the quantitative real-time PCR in comparison with the microarray data (white bars with dashed lines). The error bars represent the standard deviation of the mean ( n = 3, * P

    Article Snippet: After hybridization and washing, DNA microarrays were scanned with the Microarray Scanner (G2505 B, Agilent) as recommended by Agilent.

    Techniques: Irradiation, Real-time Polymerase Chain Reaction, Microarray, Standard Deviation

    Selectivity and sensitivity of carB -based oligonucleotide microarray.

    Journal: Applied and Environmental Microbiology

    Article Title: Specific Discrimination of Three Pathogenic Salmonella enterica subsp. enterica Serotypes by carB-Based Oligonucleotide Microarray

    doi: 10.1128/AEM.02978-13

    Figure Lengend Snippet: Selectivity and sensitivity of carB -based oligonucleotide microarray.

    Article Snippet: Prehybridization for the constructed oligonucleotide microarray was performed in buffer containing 3× SSC solution (450 mM NaCl and 3 mM trisodium citrate [pH 7.0]) with 1% (wt/vol) bovine serum albumin (BSA) (Sigma, St. Louis, MO) and 0.1% (wt/vol) sodium dodecyl sulfate (SDS) for 30 min at 50°C.

    Techniques: Microarray

    Detection of three S. enterica subsp. enterica serotypes using the carB -based oligonucleotide microarray. (A) Raw hybridization data with each amplified target at 50°C in hybridization buffer for 1 h and (B) 2D visualization plots of serotype-specific

    Journal: Applied and Environmental Microbiology

    Article Title: Specific Discrimination of Three Pathogenic Salmonella enterica subsp. enterica Serotypes by carB-Based Oligonucleotide Microarray

    doi: 10.1128/AEM.02978-13

    Figure Lengend Snippet: Detection of three S. enterica subsp. enterica serotypes using the carB -based oligonucleotide microarray. (A) Raw hybridization data with each amplified target at 50°C in hybridization buffer for 1 h and (B) 2D visualization plots of serotype-specific

    Article Snippet: Prehybridization for the constructed oligonucleotide microarray was performed in buffer containing 3× SSC solution (450 mM NaCl and 3 mM trisodium citrate [pH 7.0]) with 1% (wt/vol) bovine serum albumin (BSA) (Sigma, St. Louis, MO) and 0.1% (wt/vol) sodium dodecyl sulfate (SDS) for 30 min at 50°C.

    Techniques: Microarray, Hybridization, Amplification

    Dynamic detection range of the carB -based oligonucleotide microarray. Shown are normalized fluorescence intensity plots for the positive-control (closed circle), specific ST-1 (open circle), and specific ST-2 (closed triangle) spots according to various

    Journal: Applied and Environmental Microbiology

    Article Title: Specific Discrimination of Three Pathogenic Salmonella enterica subsp. enterica Serotypes by carB-Based Oligonucleotide Microarray

    doi: 10.1128/AEM.02978-13

    Figure Lengend Snippet: Dynamic detection range of the carB -based oligonucleotide microarray. Shown are normalized fluorescence intensity plots for the positive-control (closed circle), specific ST-1 (open circle), and specific ST-2 (closed triangle) spots according to various

    Article Snippet: Prehybridization for the constructed oligonucleotide microarray was performed in buffer containing 3× SSC solution (450 mM NaCl and 3 mM trisodium citrate [pH 7.0]) with 1% (wt/vol) bovine serum albumin (BSA) (Sigma, St. Louis, MO) and 0.1% (wt/vol) sodium dodecyl sulfate (SDS) for 30 min at 50°C.

    Techniques: Microarray, Fluorescence, Positive Control

    Schematic diagrams of (A) the regions of the carB gene used in the design of the Salmonella positive-control and serotype-specific capture probes and (B) the repeated array format for the carB -based oligonucleotide microarray.

    Journal: Applied and Environmental Microbiology

    Article Title: Specific Discrimination of Three Pathogenic Salmonella enterica subsp. enterica Serotypes by carB-Based Oligonucleotide Microarray

    doi: 10.1128/AEM.02978-13

    Figure Lengend Snippet: Schematic diagrams of (A) the regions of the carB gene used in the design of the Salmonella positive-control and serotype-specific capture probes and (B) the repeated array format for the carB -based oligonucleotide microarray.

    Article Snippet: Prehybridization for the constructed oligonucleotide microarray was performed in buffer containing 3× SSC solution (450 mM NaCl and 3 mM trisodium citrate [pH 7.0]) with 1% (wt/vol) bovine serum albumin (BSA) (Sigma, St. Louis, MO) and 0.1% (wt/vol) sodium dodecyl sulfate (SDS) for 30 min at 50°C.

    Techniques: Positive Control, Microarray

    Cationic polythiophene transducer for the fluorometric detection of hybridization on microarrays. A) Schematic depiction of the interaction between cationic polymers and a) single-stranded DNA, b) double-stranded DNA, c) single-stranded PNA and d) PNA-DNA duplex. Fluorescent cationic polymer is shown in yellow, DNA probes are shown in green and PNA probes are shown in red. B) Experimental results for fluorometric detection on microarray when cationic polythiophene transducer is reacted with a) single-stranded DNA, b) double-stranded DNA, c) single-stranded PNA and d) PNA-DNA duplex. Results are shown in triplicate. C) Graphs showing the fluorescence intensity with standard deviation for each triplicate shown in B.

    Journal: BMC Biotechnology

    Article Title: Detection of target DNA using fluorescent cationic polymer and peptide nucleic acid probes on solid support

    doi: 10.1186/1472-6750-5-10

    Figure Lengend Snippet: Cationic polythiophene transducer for the fluorometric detection of hybridization on microarrays. A) Schematic depiction of the interaction between cationic polymers and a) single-stranded DNA, b) double-stranded DNA, c) single-stranded PNA and d) PNA-DNA duplex. Fluorescent cationic polymer is shown in yellow, DNA probes are shown in green and PNA probes are shown in red. B) Experimental results for fluorometric detection on microarray when cationic polythiophene transducer is reacted with a) single-stranded DNA, b) double-stranded DNA, c) single-stranded PNA and d) PNA-DNA duplex. Results are shown in triplicate. C) Graphs showing the fluorescence intensity with standard deviation for each triplicate shown in B.

    Article Snippet: DNA microarray hybridization, polymeric detection and data acquisition Prehybridization and hybridization were performed in 15 × 13 mm Hybri-well self-sticking hybridization chambers (Sigma-Aldrich).

    Techniques: Hybridization, Microarray, Fluorescence, Standard Deviation

    HPC5, an hMOF target gene, is frequently downregulated in ovarian cancer tissues. (A) A reduction in HCP5 mRNA expression levels in hMOF siRNA knockdown cells. HeLa cells were transfected with hMOF or NT siRNAs. Following 48 h of transfection, the mRNA levels of HCP5 and actin were measured by qPCR. Error bars represent the standard error of the mean of three independent experiments. (B and C) hMOF colocalizes with H4K16Ac at HCP5 promoter. ChIP assays using transfected hMOF or NT siRNA HeLa cells were analyzed by qPCR. Bar graphs show the ratio of ChIP signals that were normalized to the input DNA. (D) HCP5 mRNA expression patterns in ovarian cancer tissues. 28 randomly selected clinical ovarian cancer and contralateral normal tissues were used. The HCP5 and hMOF mRNA expression levels in ovarian cancer were analyzed by qPCR. The y-axis indicates the log2 value of the ratio of HCP5 and hMOF expression levels between the cancer and normal tissues from the same patients. (E) Statistical analysis of qPCR results. Each bar represents the mean of three independent experiments. The significant difference is expressed as * P

    Journal: Oncology Letters

    Article Title: A potential diagnostic marker for ovarian cancer: Involvement of the histone acetyltransferase, human males absent on the first

    doi: 10.3892/ol.2013.1380

    Figure Lengend Snippet: HPC5, an hMOF target gene, is frequently downregulated in ovarian cancer tissues. (A) A reduction in HCP5 mRNA expression levels in hMOF siRNA knockdown cells. HeLa cells were transfected with hMOF or NT siRNAs. Following 48 h of transfection, the mRNA levels of HCP5 and actin were measured by qPCR. Error bars represent the standard error of the mean of three independent experiments. (B and C) hMOF colocalizes with H4K16Ac at HCP5 promoter. ChIP assays using transfected hMOF or NT siRNA HeLa cells were analyzed by qPCR. Bar graphs show the ratio of ChIP signals that were normalized to the input DNA. (D) HCP5 mRNA expression patterns in ovarian cancer tissues. 28 randomly selected clinical ovarian cancer and contralateral normal tissues were used. The HCP5 and hMOF mRNA expression levels in ovarian cancer were analyzed by qPCR. The y-axis indicates the log2 value of the ratio of HCP5 and hMOF expression levels between the cancer and normal tissues from the same patients. (E) Statistical analysis of qPCR results. Each bar represents the mean of three independent experiments. The significant difference is expressed as * P

    Article Snippet: RNAi treatment and DNA microarray HeLa cells were cultured in 6-well tissue culture plates (∼2×105 cells/well) in DMEM medium (Sigma) containing 5% glucose and 10% fetal bovine serum.

    Techniques: Expressing, Transfection, Real-time Polymerase Chain Reaction, Chromatin Immunoprecipitation

    Microarray analysis of DDC-regulated genes . Experimental outline of microarray studies to identify DDC downstream targets using LNCaP-DDC stable and control LNCaP-pDEST cells. In the presence of Dox ( grey triangle , + Dox) the tetracycline Tet repressor (tetR) is released from the TetO2 sequence in the promoter of the lentiviral construct containing the DDC gene. The dissociation of the tetR allows induction of transcription for the gene of interest. LNCaP-DDC and LNCaP-pDEST (vector control) cell lines were plated in medium containing 5% charcoal-stripped serum and incubated overnight. The next day, cells were treated for 48 hours under mock-induced (-Dox) and Dox-induced (+Dox) conditions, 24 h of which was in the presence or absence of 0.1 nM R1881. Total RNA samples were isolated from each condition, labeled and hybridized on the microarrays. The relative mRNA abundance of each gene was calculated as a ratio between hormone-treated (+R1881) and hormone-untreated (- R1881) samples. The comparison of the expression data obtained from LNCaP-DDC+Dox stable cells ( left ) with the expression data from the three LNCaP control cells ( right : LNCaP-DDC-Dox, LNCaP-pDEST- Dox, and LNCaP-pDEST+Dox) yielded the identification of genes that are androgen- and DDC-regulated.

    Journal: Molecular Cancer

    Article Title: Androgen-regulated genes differentially modulated by the androgen receptor coactivator L-dopa decarboxylase in human prostate cancer cells

    doi: 10.1186/1476-4598-6-38

    Figure Lengend Snippet: Microarray analysis of DDC-regulated genes . Experimental outline of microarray studies to identify DDC downstream targets using LNCaP-DDC stable and control LNCaP-pDEST cells. In the presence of Dox ( grey triangle , + Dox) the tetracycline Tet repressor (tetR) is released from the TetO2 sequence in the promoter of the lentiviral construct containing the DDC gene. The dissociation of the tetR allows induction of transcription for the gene of interest. LNCaP-DDC and LNCaP-pDEST (vector control) cell lines were plated in medium containing 5% charcoal-stripped serum and incubated overnight. The next day, cells were treated for 48 hours under mock-induced (-Dox) and Dox-induced (+Dox) conditions, 24 h of which was in the presence or absence of 0.1 nM R1881. Total RNA samples were isolated from each condition, labeled and hybridized on the microarrays. The relative mRNA abundance of each gene was calculated as a ratio between hormone-treated (+R1881) and hormone-untreated (- R1881) samples. The comparison of the expression data obtained from LNCaP-DDC+Dox stable cells ( left ) with the expression data from the three LNCaP control cells ( right : LNCaP-DDC-Dox, LNCaP-pDEST- Dox, and LNCaP-pDEST+Dox) yielded the identification of genes that are androgen- and DDC-regulated.

    Article Snippet: Microarrays were hybridized with 10 μg of total RNA from duplicate samples of LNCaP-DDC or LNCaP-pDEST cells treated with or without (±) Dox, and with or without (±) R1881, using the 3DNA Array 350™ Expression Array Detection Kit and according to the manufacturer's instructions (Genisphere, Hatfield, PA) (Figure ).

    Techniques: Microarray, Sequencing, Construct, Plasmid Preparation, Incubation, Isolation, Labeling, Expressing

    Identification of p53-regulated lncRNAs. ( A ) Isogenic p53-WT and p53-KO HCT116 cells were untreated or treated with Nutlin-3 for 8 hr and immunoblotting was performed for p53 and the loading control GAPDH. ( B ) Heat map is shown for the differentially expressed mRNAs and lncRNAs identified by microarrays performed in duplicate from HCT116, SW48 and RKO cells untreated or treated with Nutlin-3 for 8 hr. Upregulated genes are shown in red and downregulated genes in green. PINCR ( RP3-326I13.1 ) is shown in the red box. ( C ) Venn diagram showing the overlap between the transcriptomes upregulated ≥1.5-fold after Nutlin-3 treatment of HCT116, SW48 and RKO cells. DOI: http://dx.doi.org/10.7554/eLife.23244.004 10.7554/eLife.23244.005 p53 immunoblot for Figure 1—figure supplement 1A . DOI: http://dx.doi.org/10.7554/eLife.23244.005

    Journal: eLife

    Article Title: Prosurvival long noncoding RNA PINCR regulates a subset of p53 targets in human colorectal cancer cells by binding to Matrin 3

    doi: 10.7554/eLife.23244

    Figure Lengend Snippet: Identification of p53-regulated lncRNAs. ( A ) Isogenic p53-WT and p53-KO HCT116 cells were untreated or treated with Nutlin-3 for 8 hr and immunoblotting was performed for p53 and the loading control GAPDH. ( B ) Heat map is shown for the differentially expressed mRNAs and lncRNAs identified by microarrays performed in duplicate from HCT116, SW48 and RKO cells untreated or treated with Nutlin-3 for 8 hr. Upregulated genes are shown in red and downregulated genes in green. PINCR ( RP3-326I13.1 ) is shown in the red box. ( C ) Venn diagram showing the overlap between the transcriptomes upregulated ≥1.5-fold after Nutlin-3 treatment of HCT116, SW48 and RKO cells. DOI: http://dx.doi.org/10.7554/eLife.23244.004 10.7554/eLife.23244.005 p53 immunoblot for Figure 1—figure supplement 1A . DOI: http://dx.doi.org/10.7554/eLife.23244.005

    Article Snippet: RNA samples were prepared as described above in triplicates and labeled using the IlluminaTotalPrep RNA amplification kit (Ambion) and microarrays were performed with the HumanHT-12 v4 Expression BeadChip kit (Illumina).

    Techniques:

    Loss of PINCR results in impaired induction of a subset of p53 targets without altering induction of p53 levels. ( A ) Gene set enrichment analysis (GSEA) for the genes upregulated in the microarrays performed in biological triplicates from untreated or 5-FU-treated PINCR -WT and PINCR -KO cells. ( B ) PINCR -WT and PINCR -KO cells were untreated or treated with 5-FU for 24 hr and immunoblotting for p53 and loading control GAPDH was performed. DOI: http://dx.doi.org/10.7554/eLife.23244.030 10.7554/eLife.23244.031 p53 immunoblot for Figure 4—figure supplement 1B . DOI: http://dx.doi.org/10.7554/eLife.23244.031

    Journal: eLife

    Article Title: Prosurvival long noncoding RNA PINCR regulates a subset of p53 targets in human colorectal cancer cells by binding to Matrin 3

    doi: 10.7554/eLife.23244

    Figure Lengend Snippet: Loss of PINCR results in impaired induction of a subset of p53 targets without altering induction of p53 levels. ( A ) Gene set enrichment analysis (GSEA) for the genes upregulated in the microarrays performed in biological triplicates from untreated or 5-FU-treated PINCR -WT and PINCR -KO cells. ( B ) PINCR -WT and PINCR -KO cells were untreated or treated with 5-FU for 24 hr and immunoblotting for p53 and loading control GAPDH was performed. DOI: http://dx.doi.org/10.7554/eLife.23244.030 10.7554/eLife.23244.031 p53 immunoblot for Figure 4—figure supplement 1B . DOI: http://dx.doi.org/10.7554/eLife.23244.031

    Article Snippet: RNA samples were prepared as described above in triplicates and labeled using the IlluminaTotalPrep RNA amplification kit (Ambion) and microarrays were performed with the HumanHT-12 v4 Expression BeadChip kit (Illumina).

    Techniques:

    Array- based Nuclear Run-on (ANRO) shows consistent results between Affymetrix exon arrays and Illumina BeadChips. ( a ) Pearson's Correlation Matrix of changes in gene expression (log ratios) between tet treated (T) and untreated (UT) P493-6 human B cells following 48 hr induction for a common pool of approximately 7800 genes as measured on both Illumina BeadArrays and Affymetrix Exon microarray platforms. ( b ) heat map illustrating a selection of the highest scoring pathways using Gene Set Matrix Analysis (GSMA) on the logratios from ( a ). ( c ) Pathway breakout from b on a gene by gene basis for the Inteferon a, b Response Genes. Log ratios sorted descending on the NRO as measured on the Illumina platform ((ILL T-UT NRO).

    Journal: PLoS ONE

    Article Title: Time-Dependent c-Myc Transactomes Mapped by Array-Based Nuclear Run-On Reveal Transcriptional Modules in Human B Cells

    doi: 10.1371/journal.pone.0009691

    Figure Lengend Snippet: Array- based Nuclear Run-on (ANRO) shows consistent results between Affymetrix exon arrays and Illumina BeadChips. ( a ) Pearson's Correlation Matrix of changes in gene expression (log ratios) between tet treated (T) and untreated (UT) P493-6 human B cells following 48 hr induction for a common pool of approximately 7800 genes as measured on both Illumina BeadArrays and Affymetrix Exon microarray platforms. ( b ) heat map illustrating a selection of the highest scoring pathways using Gene Set Matrix Analysis (GSMA) on the logratios from ( a ). ( c ) Pathway breakout from b on a gene by gene basis for the Inteferon a, b Response Genes. Log ratios sorted descending on the NRO as measured on the Illumina platform ((ILL T-UT NRO).

    Article Snippet: This observation indicates that we have optimized the conditions and that the primer concentration for NRO is not a limiting factor with the Illumina microarray.

    Techniques: Expressing, Microarray, Selection

    Array- based Nuclear Run-on (ANRO) characterization. ( a, b ) Transcriptional regulation of CD69 in NRO RNA following Jurkat T Cell activation. ( a ) Illumina microarray - CD69 average signal intensity for 4 independent experiments. ( b ) CD 69 Real time PCR validation for the same experiments (fold changes were normalized by GAPDH controls). ( c, d ) RT-PCR estimates of varying amplicon size and complexity for CD69 gene transcription in PMA + I activated Jurkat T cell NRO RNA. ( c ) Fold changes for CD69 in NRO RNA were tested using either first strand cDNA or the final amplified cRNA product (as indicated). Multiple amplicons of GAPDH were similarly tested as an uninduced control. ( d ) CD69 amplicon primer design spans exon-intron genomic sequences of sizes as indicated (primer sequences are reported in Materials and Methods ). Note the location of the Illumina microarray probe located at the 3′UTR.

    Journal: PLoS ONE

    Article Title: Time-Dependent c-Myc Transactomes Mapped by Array-Based Nuclear Run-On Reveal Transcriptional Modules in Human B Cells

    doi: 10.1371/journal.pone.0009691

    Figure Lengend Snippet: Array- based Nuclear Run-on (ANRO) characterization. ( a, b ) Transcriptional regulation of CD69 in NRO RNA following Jurkat T Cell activation. ( a ) Illumina microarray - CD69 average signal intensity for 4 independent experiments. ( b ) CD 69 Real time PCR validation for the same experiments (fold changes were normalized by GAPDH controls). ( c, d ) RT-PCR estimates of varying amplicon size and complexity for CD69 gene transcription in PMA + I activated Jurkat T cell NRO RNA. ( c ) Fold changes for CD69 in NRO RNA were tested using either first strand cDNA or the final amplified cRNA product (as indicated). Multiple amplicons of GAPDH were similarly tested as an uninduced control. ( d ) CD69 amplicon primer design spans exon-intron genomic sequences of sizes as indicated (primer sequences are reported in Materials and Methods ). Note the location of the Illumina microarray probe located at the 3′UTR.

    Article Snippet: This observation indicates that we have optimized the conditions and that the primer concentration for NRO is not a limiting factor with the Illumina microarray.

    Techniques: Activation Assay, Microarray, Real-time Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Amplification, Genomic Sequencing

    Affymetrix and Illumina data from the Microarray Quality Control project can be directly integrated. A ) Pairwise Pearson correlation heatmaps (left) demonstrate cross platform bias and the effects of three correction methods, mean-centering, distance-weighted discrimination (DWD) and an Empirical Bayes method (ComBat). R values range from low correlation (red) to high correlation (white) through shades of orange and yellow reflecting the overall similarity of expression profiles based upon biological and platform-specific variation. The shades of purple to pink indicate the samples (A = 100% UHRR, B = 100% HBRR, C = 75% UHRR + 25% HBRR, D = 25% UHRR + 75% HBRR). Samples are ordered by replicate and lab name rather than by platform. Green bars for Affymetrix samples and blue for Illumina samples. Boxplots of correlation coefficients within and between labs are shown in (Additional file 1 . B ) Cross-platform correction minimises technical variation whilst maintaining biological variation and differential expression. C ) Venn diagrams demonstrate the overlap between the 1000 most differentially expressed genes between the MAQC UHRR and HBRR (A and B samples) using significance analysis of Microarrays (SAM) method with either Affymetrix (Green) or Illumina (Blue) alone, or Affymetrix and Illumina together (Purple).

    Journal: BMC Medical Genomics

    Article Title: Direct integration of intensity-level data from Affymetrix and Illumina microarrays improves statistical power for robust reanalysis

    doi: 10.1186/1755-8794-5-35

    Figure Lengend Snippet: Affymetrix and Illumina data from the Microarray Quality Control project can be directly integrated. A ) Pairwise Pearson correlation heatmaps (left) demonstrate cross platform bias and the effects of three correction methods, mean-centering, distance-weighted discrimination (DWD) and an Empirical Bayes method (ComBat). R values range from low correlation (red) to high correlation (white) through shades of orange and yellow reflecting the overall similarity of expression profiles based upon biological and platform-specific variation. The shades of purple to pink indicate the samples (A = 100% UHRR, B = 100% HBRR, C = 75% UHRR + 25% HBRR, D = 25% UHRR + 75% HBRR). Samples are ordered by replicate and lab name rather than by platform. Green bars for Affymetrix samples and blue for Illumina samples. Boxplots of correlation coefficients within and between labs are shown in (Additional file 1 . B ) Cross-platform correction minimises technical variation whilst maintaining biological variation and differential expression. C ) Venn diagrams demonstrate the overlap between the 1000 most differentially expressed genes between the MAQC UHRR and HBRR (A and B samples) using significance analysis of Microarrays (SAM) method with either Affymetrix (Green) or Illumina (Blue) alone, or Affymetrix and Illumina together (Purple).

    Article Snippet: Considering the fundamental differences in the design of the two platforms, it is not clear whether data derived from Affymetrix and Illumina microarrays can be reliably compared directly.

    Techniques: Microarray, Expressing

    Genomewide expression changes induced by Egr-2. Fibroblasts were transfected with Ad-GFP or Ad–Egr-2 or left untransfected (control) for 48 hours before RNA isolation and processing for microarray analysis. A: Heat map. The genes that showed greater

    Journal: The American Journal of Pathology

    Article Title: The Early Growth Response Gene Egr2 (Alias Krox20) Is a Novel Transcriptional Target of Transforming Growth Factor-? that Is Up-Regulated in Systemic Sclerosis and Mediates Profibrotic Responses

    doi: 10.1016/j.ajpath.2011.01.035

    Figure Lengend Snippet: Genomewide expression changes induced by Egr-2. Fibroblasts were transfected with Ad-GFP or Ad–Egr-2 or left untransfected (control) for 48 hours before RNA isolation and processing for microarray analysis. A: Heat map. The genes that showed greater

    Article Snippet: Fluorescently labeled cDNA was prepared using labeling kits (Ambion, Austin, TX), followed by hybridization to microarray chips (Illumina Human HT-12 Version 3) containing 44,000 probes (Illumina, San Diego, CA).

    Techniques: Expressing, Transfection, Isolation, Microarray

    Expressed pattern of miRNAs in five tissues of Acipenser schrenckii . The expression of 58 miRNAs detected by microarray (Signal > 500 and P ≤0.01) are reflected by Log-normalized intensities. Heat map represents the miRNAs which were clustered into two clades based on their expression in tissues.

    Journal: PLoS ONE

    Article Title: High-Throughput Sequencing of MicroRNA Transcriptome and Expression Assay in the Sturgeon, Acipenser schrenckii

    doi: 10.1371/journal.pone.0115251

    Figure Lengend Snippet: Expressed pattern of miRNAs in five tissues of Acipenser schrenckii . The expression of 58 miRNAs detected by microarray (Signal > 500 and P ≤0.01) are reflected by Log-normalized intensities. Heat map represents the miRNAs which were clustered into two clades based on their expression in tissues.

    Article Snippet: Expression pattern assay of miRNAs by microarray and real-time PCR We used the independent microarray platform to validate the expression level of 103 miRNAs obtained by Illumina TruSeq sequencing.

    Techniques: Expressing, Microarray

    Comparison of genotype concordances with SNP microarray. The x-axis shows the depth of each WGS data in a logarithmic scale. The y-axis corresponds to each metric of Fig. 3B . ( A ) CR based on depths. With the settings of HC and VQSR (blue line), > 13.7× depth achieved as high as > 99% of concordances (ocher broken line), whereas HC and HF (the red line), > 21.9× depth achieved. ( B ) FPR based on depths. ( C ) FNR based on depths. ( D ) NTPR based on depths. With both filtration procedures of HF and VQSR, > 9.8× depth achieved as high as > 99% of NTPR (ocher line).

    Journal: Scientific Reports

    Article Title: Empirical evaluation of variant calling accuracy using ultra-deep whole-genome sequencing data

    doi: 10.1038/s41598-018-38346-0

    Figure Lengend Snippet: Comparison of genotype concordances with SNP microarray. The x-axis shows the depth of each WGS data in a logarithmic scale. The y-axis corresponds to each metric of Fig. 3B . ( A ) CR based on depths. With the settings of HC and VQSR (blue line), > 13.7× depth achieved as high as > 99% of concordances (ocher broken line), whereas HC and HF (the red line), > 21.9× depth achieved. ( B ) FPR based on depths. ( C ) FNR based on depths. ( D ) NTPR based on depths. With both filtration procedures of HF and VQSR, > 9.8× depth achieved as high as > 99% of NTPR (ocher line).

    Article Snippet: Concordance comparisons with SNP microarray data or the WGS data with all the reads We obtained genome-wide SNP genotypes of the same individual by using SNP microarray (Illumina HumanOmniExpressExome-8 v1.2) as described previously , .

    Techniques: Microarray, Filtration

    Definition of the genotype concordance measurement. ( A ) Genotype concordance matrix. All combinations of the three SNV genotypes (reference / reference [Ref/Ref], reference / alterative [Ref/Alt], alternative / alternative [Alt/Alt]) between the WGS and SNP microarray were assigned. The positions were classified as false positive when alternate alleles were discordant between the sequence and the microarray data. We assessed genotypes as homo-reference that were not included in the VCF files of the WGS data. ( B ) Genotype concordance metrics. We adopted all the genotypes on the microarray as a parameter during assessment of CR, FPR, and FNR, whereas variants called in each of the WGS data were used to assess NTPR.

    Journal: Scientific Reports

    Article Title: Empirical evaluation of variant calling accuracy using ultra-deep whole-genome sequencing data

    doi: 10.1038/s41598-018-38346-0

    Figure Lengend Snippet: Definition of the genotype concordance measurement. ( A ) Genotype concordance matrix. All combinations of the three SNV genotypes (reference / reference [Ref/Ref], reference / alterative [Ref/Alt], alternative / alternative [Alt/Alt]) between the WGS and SNP microarray were assigned. The positions were classified as false positive when alternate alleles were discordant between the sequence and the microarray data. We assessed genotypes as homo-reference that were not included in the VCF files of the WGS data. ( B ) Genotype concordance metrics. We adopted all the genotypes on the microarray as a parameter during assessment of CR, FPR, and FNR, whereas variants called in each of the WGS data were used to assess NTPR.

    Article Snippet: Concordance comparisons with SNP microarray data or the WGS data with all the reads We obtained genome-wide SNP genotypes of the same individual by using SNP microarray (Illumina HumanOmniExpressExome-8 v1.2) as described previously , .

    Techniques: Microarray, Sequencing

    Comparison of the relative expression of the Wnt pathway inhibitors in healthy nonsmokers (n = 47), healthy smokers (n = 58), and smokers with COPD (n = 22). Analysis was carried out with HG-U133 plus 2.0 microarrays. Each bar represents mean expression with standard error; p values are represented in brackets above the bars.

    Journal: PLoS ONE

    Article Title: Down-Regulation of the Canonical Wnt ?-Catenin Pathway in the Airway Epithelium of Healthy Smokers and Smokers with COPD

    doi: 10.1371/journal.pone.0014793

    Figure Lengend Snippet: Comparison of the relative expression of the Wnt pathway inhibitors in healthy nonsmokers (n = 47), healthy smokers (n = 58), and smokers with COPD (n = 22). Analysis was carried out with HG-U133 plus 2.0 microarrays. Each bar represents mean expression with standard error; p values are represented in brackets above the bars.

    Article Snippet: Hybridizations to test chips and when permissible, to the microarrays, were conducted according to Affymetrix protocols.

    Techniques: Expressing

    Comparison of the relative expression of the Wnt pathway downstream and target genes in healthy nonsmokers (n = 47), healthy smokers (n = 58), and smokers with COPD (n = 22). Analysis was carried out with HG-U133 plus 2.0 microarrays normalized by chip and gene. Each bar represents mean expression with standard error; * p

    Journal: PLoS ONE

    Article Title: Down-Regulation of the Canonical Wnt ?-Catenin Pathway in the Airway Epithelium of Healthy Smokers and Smokers with COPD

    doi: 10.1371/journal.pone.0014793

    Figure Lengend Snippet: Comparison of the relative expression of the Wnt pathway downstream and target genes in healthy nonsmokers (n = 47), healthy smokers (n = 58), and smokers with COPD (n = 22). Analysis was carried out with HG-U133 plus 2.0 microarrays normalized by chip and gene. Each bar represents mean expression with standard error; * p

    Article Snippet: Hybridizations to test chips and when permissible, to the microarrays, were conducted according to Affymetrix protocols.

    Techniques: Expressing, Chromatin Immunoprecipitation

    Genes not represented on Affymetrix GeneChip microarrays identified through SSH: Out of the 1940 transcripts in H56 SSH library, 1409 are represented on the U95 series GeneChip microarrays. 333 of the transcripts have matches in the DNA sequence databases searched, but are not represented on the U95 series GeneChip microarray. 198 of the transcripts have no match in any of the DNA sequence databases searched.

    Journal: BMC Genomics

    Article Title: Comparing gene discovery from Affymetrix GeneChip microarrays and Clontech PCR-select cDNA subtraction: a case study

    doi: 10.1186/1471-2164-5-26

    Figure Lengend Snippet: Genes not represented on Affymetrix GeneChip microarrays identified through SSH: Out of the 1940 transcripts in H56 SSH library, 1409 are represented on the U95 series GeneChip microarrays. 333 of the transcripts have matches in the DNA sequence databases searched, but are not represented on the U95 series GeneChip microarray. 198 of the transcripts have no match in any of the DNA sequence databases searched.

    Article Snippet: Certain genes present in the SSH libraries and represented on GeneChip microarrays were not detected through GeneChip microarray analysis To find out how many of the SSH detected genes with probes on the GeneChip microarrays can actually be detected by the Affymetrix technology, we used the subtracted cDNA to synthesize labeled complimentary RNA (cRNA) targets for the GeneChip microarrays.

    Techniques: Sequencing, Microarray

    Comparing the SSH data with GeneChip microarray data using subtracted samples as targets. The GeneChip microarrays were screened with cRNA targets made from the same subtracted cDNA used for SSH. (a) Number of transcripts in the H56 SSH library identified as

    Journal: BMC Genomics

    Article Title: Comparing gene discovery from Affymetrix GeneChip microarrays and Clontech PCR-select cDNA subtraction: a case study

    doi: 10.1186/1471-2164-5-26

    Figure Lengend Snippet: Comparing the SSH data with GeneChip microarray data using subtracted samples as targets. The GeneChip microarrays were screened with cRNA targets made from the same subtracted cDNA used for SSH. (a) Number of transcripts in the H56 SSH library identified as "present" or "absent" on the GeneChip microarrays. (b) The copy number of each transcript in the SSH library plotted against its detectability on the GeneChip microarrays. Each dot represents a distinct transcript identified in the H56 SSH cDNA library. The transcripts that can be detected by the GeneChip microarrays were given "present" calls, while the transcripts that cannot be detected by the GeneChip microarrays were given "absent" calls.

    Article Snippet: Certain genes present in the SSH libraries and represented on GeneChip microarrays were not detected through GeneChip microarray analysis To find out how many of the SSH detected genes with probes on the GeneChip microarrays can actually be detected by the Affymetrix technology, we used the subtracted cDNA to synthesize labeled complimentary RNA (cRNA) targets for the GeneChip microarrays.

    Techniques: Microarray, cDNA Library Assay

    Comparing the SSH data with GeneChip ® data using non-subtracted RNA as targets. The GeneChip microarrays were screened with cRNA targets made from un-modified iDC and monocyte RNA samples, and the concordance of the SSH data with GeneChip data was shown when (a) all the transcripts in the H56 library were considered, or (b) when only the transcripts unique to H56 were considered, after the transcripts appeared in both H56 and the reciprocally subtracted H57 libraries were excluded.

    Journal: BMC Genomics

    Article Title: Comparing gene discovery from Affymetrix GeneChip microarrays and Clontech PCR-select cDNA subtraction: a case study

    doi: 10.1186/1471-2164-5-26

    Figure Lengend Snippet: Comparing the SSH data with GeneChip ® data using non-subtracted RNA as targets. The GeneChip microarrays were screened with cRNA targets made from un-modified iDC and monocyte RNA samples, and the concordance of the SSH data with GeneChip data was shown when (a) all the transcripts in the H56 library were considered, or (b) when only the transcripts unique to H56 were considered, after the transcripts appeared in both H56 and the reciprocally subtracted H57 libraries were excluded.

    Article Snippet: Certain genes present in the SSH libraries and represented on GeneChip microarrays were not detected through GeneChip microarray analysis To find out how many of the SSH detected genes with probes on the GeneChip microarrays can actually be detected by the Affymetrix technology, we used the subtracted cDNA to synthesize labeled complimentary RNA (cRNA) targets for the GeneChip microarrays.

    Techniques: Modification

    A , genes involved in various cellular processes were identified by microarray experiment as differentially expressed in the absence of Id2 at CT8/12, CT20, CT8, and CT12. Microarray experiments ( n = 3/genotype) at CT8, CT12, and CT20 identified genes involved in various cellular processes that are differentially expressed ≥1.3-fold change in the absence of Id2. B , 38 and 62% of genes identified as differentially expressed were up- and down-regulated, respectively, in the absence of Id2. C , distribution of Id2 −/− ).

    Journal: The Journal of Biological Chemistry

    Article Title: ID2 (Inhibitor of DNA Binding 2) Is a Rhythmically Expressed Transcriptional Repressor Required for Circadian Clock Output in Mouse Liver *

    doi: 10.1074/jbc.M109.013961

    Figure Lengend Snippet: A , genes involved in various cellular processes were identified by microarray experiment as differentially expressed in the absence of Id2 at CT8/12, CT20, CT8, and CT12. Microarray experiments ( n = 3/genotype) at CT8, CT12, and CT20 identified genes involved in various cellular processes that are differentially expressed ≥1.3-fold change in the absence of Id2. B , 38 and 62% of genes identified as differentially expressed were up- and down-regulated, respectively, in the absence of Id2. C , distribution of Id2 −/− ).

    Article Snippet: Subsequent steps including reverse transcription, labeled cDNA synthesis, hybridization onto Mouse 430 2.0 microarray chips (Affymetrix, Santa Clara, CA), and scanning of microarrays were conducted at the Dartmouth Medical School Genomics and Microarray Laboratory according to the Affymetrix manual directions.

    Techniques: Microarray

    Infiltration of immune cells into the mammary gland tissues in response to LPS infection. (A) HE staining of mouse mammary tissues at 4 h after intramammary infusion of saline and LPS (1 μg). The infiltration of inflammatory cells (dark dots) into the mammary gland tissue is evident in LPS-treated glands. Shown are representative photographs of mammary tissue sections from either three saline-treated mice or three LPS-treated mice. (B) Graphical representation of induced chemotactic factors. Shown are expression levels of induced genes that are categorized by chemokines, chemokine receptors, adhesion molecules, and chemotactants, respectively. The mean and standard error for each gene are calculated from three independent normalized hybridization intensities from the microarray data set. The number on the top of the bar of each gene represents changes ( n -fold) derived from microarray analysis.

    Journal: Infection and Immunity

    Article Title: Genome-Wide Expression Analysis of Lipopolysaccharide-Induced Mastitis in a Mouse Model †

    doi: 10.1128/IAI.74.3.1907-1915.2006

    Figure Lengend Snippet: Infiltration of immune cells into the mammary gland tissues in response to LPS infection. (A) HE staining of mouse mammary tissues at 4 h after intramammary infusion of saline and LPS (1 μg). The infiltration of inflammatory cells (dark dots) into the mammary gland tissue is evident in LPS-treated glands. Shown are representative photographs of mammary tissue sections from either three saline-treated mice or three LPS-treated mice. (B) Graphical representation of induced chemotactic factors. Shown are expression levels of induced genes that are categorized by chemokines, chemokine receptors, adhesion molecules, and chemotactants, respectively. The mean and standard error for each gene are calculated from three independent normalized hybridization intensities from the microarray data set. The number on the top of the bar of each gene represents changes ( n -fold) derived from microarray analysis.

    Article Snippet: The quality of microarray data was assessed by monitoring a series of quality control parameters as suggested by Affymetrix, including visually inspecting the array images to confirm scanner alignment and the absence of any image artifacts; determining that Affymetrix MAS 5.0 scaling factors, as well as background, Q values, and mean intensities, for all arrays were within acceptable limits; and determining that the 3′/5′ ratios for the probe sets for β-actin and GAPDH (glyceraldehyde-3-phosphate dehydrogenase) were within acceptable limits.

    Techniques: Infection, Staining, Mouse Assay, Expressing, Hybridization, Microarray, Derivative Assay

    Verification of gene expression by immunocytochemistry and real-time RT-PC. (A) Immunocytochemistry assay visualized by DAB (brown) showing the expression changes of Ambn (ameloblastin), Dsp (dentin sialoprotein), and MMP25 (matrix metallopeptidase 25) were in concordance with the results of the normalized microarray. (B) Pearson correlation analysis (R > 0.9, p

    Journal: BMC Genomics

    Article Title: Stage-specific differential gene expression profiling and functional network analysis during morphogenesis of diphyodont dentition in miniature pigs, Sus Scrofa

    doi: 10.1186/1471-2164-15-103

    Figure Lengend Snippet: Verification of gene expression by immunocytochemistry and real-time RT-PC. (A) Immunocytochemistry assay visualized by DAB (brown) showing the expression changes of Ambn (ameloblastin), Dsp (dentin sialoprotein), and MMP25 (matrix metallopeptidase 25) were in concordance with the results of the normalized microarray. (B) Pearson correlation analysis (R > 0.9, p

    Article Snippet: The RNA labeling and microarray hybridization were carried out according to the Affymetrix expression analysis technical manual (Biotechnology Corporation, Shanghai, China).

    Techniques: Expressing, Immunocytochemistry, Microarray

    Characteristics of transcriptional response in kidney and liver. Following microarray preprocessing and general-linear modeling, we explored transcriptome-wide characteristics of genes altered in kidney and liver. Because very few genes displayed AHR-independent responses to TCDD these were not included in our analyses. First, we looked at the fraction of genes that were induced (A). Genes that were responsive to TCDD in either liver or kidney, as well as those altered by Ahr genotype in kidney, are much more likely to be inductive than repressive. By contrast genes responsive to Ahr genotype in liver were balanced slightly enriched for repressive responses. Next, to study intertissue responses to TCDD, we performed a coclustering analysis (B). The strongest trend was Ahr genotype, with both TCDD exposure and tissue having effects of similar magnitude. The color bar on the right side of the heatmap indicates tissue (yellow, kidney; green, liver), Ahr genotype (blue, AHR −/− ; white, AHR +/+ ), and TCDD exposure (red, TCDD treated; white, vehicle treated).

    Journal: Toxicological Sciences

    Article Title: Dioxin-Dependent and Dioxin-Independent Gene Batteries: Comparison of Liver and Kidney in AHR-Null Mice

    doi: 10.1093/toxsci/kfp191

    Figure Lengend Snippet: Characteristics of transcriptional response in kidney and liver. Following microarray preprocessing and general-linear modeling, we explored transcriptome-wide characteristics of genes altered in kidney and liver. Because very few genes displayed AHR-independent responses to TCDD these were not included in our analyses. First, we looked at the fraction of genes that were induced (A). Genes that were responsive to TCDD in either liver or kidney, as well as those altered by Ahr genotype in kidney, are much more likely to be inductive than repressive. By contrast genes responsive to Ahr genotype in liver were balanced slightly enriched for repressive responses. Next, to study intertissue responses to TCDD, we performed a coclustering analysis (B). The strongest trend was Ahr genotype, with both TCDD exposure and tissue having effects of similar magnitude. The color bar on the right side of the heatmap indicates tissue (yellow, kidney; green, liver), Ahr genotype (blue, AHR −/− ; white, AHR +/+ ), and TCDD exposure (red, TCDD treated; white, vehicle treated).

    Article Snippet: To ensure that transcriptional profiles from our new kidney data and older liver data are directly comparable we employed the same microarray platform and hybridization protocols for the two studies (Affymetrix MOE430-2 arrays) and analyzed the datasets using identical algorithms and software versions.

    Techniques: Microarray

    Comparison of transcriptional response in kidney and liver. Following preprocessing and general-linear modeling of the microarray data, we compared the specific genes altered by Ahr genotype (A) and TCDD exposure (B) in liver and kidney. Large numbers of genes were altered by Ahr genotype in each tissue, and a significant fraction ( p

    Journal: Toxicological Sciences

    Article Title: Dioxin-Dependent and Dioxin-Independent Gene Batteries: Comparison of Liver and Kidney in AHR-Null Mice

    doi: 10.1093/toxsci/kfp191

    Figure Lengend Snippet: Comparison of transcriptional response in kidney and liver. Following preprocessing and general-linear modeling of the microarray data, we compared the specific genes altered by Ahr genotype (A) and TCDD exposure (B) in liver and kidney. Large numbers of genes were altered by Ahr genotype in each tissue, and a significant fraction ( p

    Article Snippet: To ensure that transcriptional profiles from our new kidney data and older liver data are directly comparable we employed the same microarray platform and hybridization protocols for the two studies (Affymetrix MOE430-2 arrays) and analyzed the datasets using identical algorithms and software versions.

    Techniques: Microarray

    Effects of AHR −/− on transcriptional response to TCDD in kidney and liver. Following preprocessing of the microarray data, general-linear modeling was performed separately for the kidney (A) and liver (B) data. In both cases few genes were altered by TCDD in the absence of functional AHR protein whereas large numbers of genes were responsive to Ahr genotype even in the absence of TCDD exposure. Interestingly, whereas only 17 genes were TCDD responsive in an AHR-dependent fashion in kidney, fully 297 (17-fold more) were altered in liver. To visualize interanimal variability we employed unsupervised machine-learning separately on kidney (C) and liver (D); with few exceptions interanimal variability is small, and in all cases is smaller than intergroup variability. The color bar in the heat maps represents Ahr genotype (blue, AHR −/− ; white, AHR +/+ ) and TCDD exposure (red, TCDD exposed; white, vehicle treated).

    Journal: Toxicological Sciences

    Article Title: Dioxin-Dependent and Dioxin-Independent Gene Batteries: Comparison of Liver and Kidney in AHR-Null Mice

    doi: 10.1093/toxsci/kfp191

    Figure Lengend Snippet: Effects of AHR −/− on transcriptional response to TCDD in kidney and liver. Following preprocessing of the microarray data, general-linear modeling was performed separately for the kidney (A) and liver (B) data. In both cases few genes were altered by TCDD in the absence of functional AHR protein whereas large numbers of genes were responsive to Ahr genotype even in the absence of TCDD exposure. Interestingly, whereas only 17 genes were TCDD responsive in an AHR-dependent fashion in kidney, fully 297 (17-fold more) were altered in liver. To visualize interanimal variability we employed unsupervised machine-learning separately on kidney (C) and liver (D); with few exceptions interanimal variability is small, and in all cases is smaller than intergroup variability. The color bar in the heat maps represents Ahr genotype (blue, AHR −/− ; white, AHR +/+ ) and TCDD exposure (red, TCDD exposed; white, vehicle treated).

    Article Snippet: To ensure that transcriptional profiles from our new kidney data and older liver data are directly comparable we employed the same microarray platform and hybridization protocols for the two studies (Affymetrix MOE430-2 arrays) and analyzed the datasets using identical algorithms and software versions.

    Techniques: Microarray, Functional Assay

    Experimental design. Mice harboring either the wild-type AHR (i.e., AHR +/+ ) or with genetic ablation of the AHR locus (i.e., AHR −/− ) in a C57BL/6J background were treated with either corn-oil vehicle (not indicated) or 1000 μg/kg TCDD (i.e., +TCDD). The number of mice used was six in AHR +/+ conditions and three for the AHR −/− conditions. Both liver and kidney were excised 19 h after treatment, RNA extracted, and microarray profiling of mRNA abundances performed as described in “Material and Methods.” General-linear modeling was used to identify three effects. The AHR effect (labeled as “AHR”) gives alterations in mRNA abundance dependent on Ahr genotype, even in the absence of TCDD exposure. The TCDD effect (labeled as “TCDD”) gives alterations in mRNA abundance dependent on TCDD exposure, even in AHR −/− animals. Finally the AHR-TCDD interaction (labeled as “AHR:TCDD”) gives effects dependent on both Ahr genotype and TCDD exposure.

    Journal: Toxicological Sciences

    Article Title: Dioxin-Dependent and Dioxin-Independent Gene Batteries: Comparison of Liver and Kidney in AHR-Null Mice

    doi: 10.1093/toxsci/kfp191

    Figure Lengend Snippet: Experimental design. Mice harboring either the wild-type AHR (i.e., AHR +/+ ) or with genetic ablation of the AHR locus (i.e., AHR −/− ) in a C57BL/6J background were treated with either corn-oil vehicle (not indicated) or 1000 μg/kg TCDD (i.e., +TCDD). The number of mice used was six in AHR +/+ conditions and three for the AHR −/− conditions. Both liver and kidney were excised 19 h after treatment, RNA extracted, and microarray profiling of mRNA abundances performed as described in “Material and Methods.” General-linear modeling was used to identify three effects. The AHR effect (labeled as “AHR”) gives alterations in mRNA abundance dependent on Ahr genotype, even in the absence of TCDD exposure. The TCDD effect (labeled as “TCDD”) gives alterations in mRNA abundance dependent on TCDD exposure, even in AHR −/− animals. Finally the AHR-TCDD interaction (labeled as “AHR:TCDD”) gives effects dependent on both Ahr genotype and TCDD exposure.

    Article Snippet: To ensure that transcriptional profiles from our new kidney data and older liver data are directly comparable we employed the same microarray platform and hybridization protocols for the two studies (Affymetrix MOE430-2 arrays) and analyzed the datasets using identical algorithms and software versions.

    Techniques: Mouse Assay, Microarray, Labeling

    Microarray transcriptome analysis of rat hepatocytes with different ploidy statuses. ( A ) Heatmap with hierarchical clustering of whole-transcriptome analysis of 18,601 probes. Experiments were performed with 5 rats. ( B ) Expression of general hepatocyte marker genes. Data are means ± SEM (n = 5). ( C ) 8c hepatocyte-enriched pathways with GO terms (biological process) are shown. Dots represent term enrichment with color coding. The sizes of the dots represent the percentage of each GO term. ( D ) Gene signature enrichment analysis of 8c hepatocytes and 2c and 4c hepatocytes using the KEGG cell-cycle gene set. ( E ) Expression of cell cycle–related genes. Data are means ± SEM (n = 5). ( B and E ) Bottom: P values were calculated by RM 1-way ANOVA, followed by the Holm multiple comparisons test. P values for post hoc tests are presented as follows: * P

    Journal: Cellular and Molecular Gastroenterology and Hepatology

    Article Title: Transcriptomic Dissection of Hepatocyte Heterogeneity: Linking Ploidy, Zonation, and Stem/Progenitor Cell Characteristics

    doi: 10.1016/j.jcmgh.2019.08.011

    Figure Lengend Snippet: Microarray transcriptome analysis of rat hepatocytes with different ploidy statuses. ( A ) Heatmap with hierarchical clustering of whole-transcriptome analysis of 18,601 probes. Experiments were performed with 5 rats. ( B ) Expression of general hepatocyte marker genes. Data are means ± SEM (n = 5). ( C ) 8c hepatocyte-enriched pathways with GO terms (biological process) are shown. Dots represent term enrichment with color coding. The sizes of the dots represent the percentage of each GO term. ( D ) Gene signature enrichment analysis of 8c hepatocytes and 2c and 4c hepatocytes using the KEGG cell-cycle gene set. ( E ) Expression of cell cycle–related genes. Data are means ± SEM (n = 5). ( B and E ) Bottom: P values were calculated by RM 1-way ANOVA, followed by the Holm multiple comparisons test. P values for post hoc tests are presented as follows: * P

    Article Snippet: Inconsistencies between their observations and ours might derive from differences in, first, the analyzed probe numbers: approximately 12,000 probes (designed based on the information available in 2002) were included in the Lu et al study, whereas approximately 45,000 probes were used in our study; and, second, the microarray platforms: Lu et al used the Affymetrix (Santa Clara, CA) platform, whereas we used the Agilent platform.

    Techniques: Microarray, Expressing, Marker

    Heatmap analysis of microarray data showing hierarchical clustering of 832 differentially expressed genes between first trimester primary trophoblasts, AC1-1 and ACH-3P cells . Three first trimester primary trophoblast preparations (FT 1, 2, 3), two AC1-1 (AC1-1 1, 2) and two ACH-3P (ACH-3P 1, 2) RNA preparations were analyzed. Red or green colours indicate differentially up- or downregulated (619) genes, respectively (FC > 2 fold). The dendrogram displayed on top was based on hierarchical clustering of the samples using the average linkage method indicating the strong relation of the ACH3P cell line with the primary cells.

    Journal: BMC Developmental Biology

    Article Title: The first trimester human trophoblast cell line ACH-3P: A novel tool to study autocrine/paracrine regulatory loops of human trophoblast subpopulations - TNF-? stimulates MMP15 expression

    doi: 10.1186/1471-213X-7-137

    Figure Lengend Snippet: Heatmap analysis of microarray data showing hierarchical clustering of 832 differentially expressed genes between first trimester primary trophoblasts, AC1-1 and ACH-3P cells . Three first trimester primary trophoblast preparations (FT 1, 2, 3), two AC1-1 (AC1-1 1, 2) and two ACH-3P (ACH-3P 1, 2) RNA preparations were analyzed. Red or green colours indicate differentially up- or downregulated (619) genes, respectively (FC > 2 fold). The dendrogram displayed on top was based on hierarchical clustering of the samples using the average linkage method indicating the strong relation of the ACH3P cell line with the primary cells.

    Article Snippet: Raw data were normalized globally and processed with Microarray Suite (MAS 5.0, Affymetrix) and Data Mining Tool (DMT, Affymetrix).

    Techniques: Microarray

    Copy number analysis of 15 marker regions (see Table 2) . A: Kaplan Meier estimates of progression free survival according to number of copy-number imbalanced marker regions in QPCR analysis. Stable (0–2 changes); intermediate (3–4 changes), unstable ( > 4 changes). B: Copy number alterations (log2 ratios) of candidate regions determined by SNP microarrays (SNPs flanking the marker regions). Tumors in columns, marker regions in rows. Top row indicates patient and tumor ID, bars below refer to tumor characteristics. Non-progressors to the left, progressors to the right; stage T1 tumors in the middle, stage Ta tumors on the flanks. Tumors are further sorted according to their CIS status: Tumors with concomitant CIS in the very center and on the very verges, tumors with later or no CIS in between. Furthermore, the grade of dysplasia (Bergkvist[ 15 ]), the actual clinical risk (including previous history)[ 3 ] and the used microarray (1 = 50 K, 2 = 10 K) are indicated. Data area: Red: Copy number gain. Blue: Copy number loss. C: Copy number analysis of the same candidate regions by QPCR of 101 tumors, hereof 77 independent tumors. Tumors are sorted in the same way as in B . A survey of the number of altered regions is provided in Additional File 7 .

    Journal: BMC Cancer

    Article Title: Chromosomal imbalance in the progression of high-risk non-muscle invasive bladder cancer

    doi: 10.1186/1471-2407-9-149

    Figure Lengend Snippet: Copy number analysis of 15 marker regions (see Table 2) . A: Kaplan Meier estimates of progression free survival according to number of copy-number imbalanced marker regions in QPCR analysis. Stable (0–2 changes); intermediate (3–4 changes), unstable ( > 4 changes). B: Copy number alterations (log2 ratios) of candidate regions determined by SNP microarrays (SNPs flanking the marker regions). Tumors in columns, marker regions in rows. Top row indicates patient and tumor ID, bars below refer to tumor characteristics. Non-progressors to the left, progressors to the right; stage T1 tumors in the middle, stage Ta tumors on the flanks. Tumors are further sorted according to their CIS status: Tumors with concomitant CIS in the very center and on the very verges, tumors with later or no CIS in between. Furthermore, the grade of dysplasia (Bergkvist[ 15 ]), the actual clinical risk (including previous history)[ 3 ] and the used microarray (1 = 50 K, 2 = 10 K) are indicated. Data area: Red: Copy number gain. Blue: Copy number loss. C: Copy number analysis of the same candidate regions by QPCR of 101 tumors, hereof 77 independent tumors. Tumors are sorted in the same way as in B . A survey of the number of altered regions is provided in Additional File 7 .

    Article Snippet: We previously analysed tumors from 19 patients from this cohort using Affymetrix® Early Access GeneChip® Mapping 10 K SNP microarrays (Affymetrix, Santa Clara, CA) [ , ].

    Techniques: Marker, Real-time Polymerase Chain Reaction, Microarray

    Transcriptome-wide identification of HuR-associated circRNAs. (A,B) Schematic of the strategy used to identify globally HuR-interacting circRNAs in HeLa cells (A). Following cell lysis, RIP analysis was carried out using anti-HuR or control IgG antibodies; the presence of HuR in the IP samples was assessed by Western blot analysis [(B); HC, heavy IgG chain]. Total RNA was isolated and digested with RNase R, and circRNAs present in the sample were identified using circRNA microarrays (Arraystar). (C) Partial list of circRNAs highly enriched in HuR IP relative to IgG IP as identified in microarrays (n = 3).

    Journal: RNA Biology

    Article Title: Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by CircPABPN1

    doi: 10.1080/15476286.2017.1279788

    Figure Lengend Snippet: Transcriptome-wide identification of HuR-associated circRNAs. (A,B) Schematic of the strategy used to identify globally HuR-interacting circRNAs in HeLa cells (A). Following cell lysis, RIP analysis was carried out using anti-HuR or control IgG antibodies; the presence of HuR in the IP samples was assessed by Western blot analysis [(B); HC, heavy IgG chain]. Total RNA was isolated and digested with RNase R, and circRNAs present in the sample were identified using circRNA microarrays (Arraystar). (C) Partial list of circRNAs highly enriched in HuR IP relative to IgG IP as identified in microarrays (n = 3).

    Article Snippet: Endogenous circRNAs associated with HuR were identified by RIP analysis as described extracted using TRIzol, and identified using microarrays (Arraystar).

    Techniques: Lysis, Western Blot, Isolation

    ) was hybridized to tiling microarrays together with in vitro ) have been excluded because nucleosome spacing is different in these regions. Dotted lines at multiples of the estimated nucleosome repeat length (NRL) indicate positions of peaks and valleys corresponding to nucleosomes and linker DNA in white (black) and H3.3 (grey) knockdown cells.

    Journal: The EMBO Journal

    Article Title: Histone H1 binding is inhibited by histone variant H3.3

    doi: 10.1038/emboj.2009.301

    Figure Lengend Snippet: ) was hybridized to tiling microarrays together with in vitro ) have been excluded because nucleosome spacing is different in these regions. Dotted lines at multiples of the estimated nucleosome repeat length (NRL) indicate positions of peaks and valleys corresponding to nucleosomes and linker DNA in white (black) and H3.3 (grey) knockdown cells.

    Article Snippet: In vivo methylated DNA was amplified as described earlier ( ) and hybridized to microarrays carrying 380 000 60-mer DNA oligos ( ) (Roche-NimbleGen).

    Techniques: In Vitro

    S. mansoni gDNA has superior hybridization characteristics compared to S. mansoni cDNA. The use of S. mansoni gDNA as a common reference reveals higher median intensity values and narrower overall intensity distributions than a complex S. mansoni cDNA reference. Box-plots display signal intensities for the AF-555 channel for S. japonicum , S. mansoni , M. musculus gDNA and complex reference S. mansoni cDNA pool (as described in Methods ). Boxes represent three independent experiments for mouse gDNA, S. mansoni gDNA and S. mansoni cDNA pool, respectively. S. japonicum gDNA is represented by a single experiment. All negative control microarray signals were removed before analysis, microarrays were filtered for manually excluded spots and each experiment was subsequently filtered to contain the same number of spots (n = 32,746). Statistical significance was defined using a Student's t-test between three independently replicated experiments. Horizontal lines represent median oligonucleotide intensity, boxes display oligonucleotide elements 25% above and below the median value and whiskers show oligonucleotide elements within 1.5 deviations of the median. Outlier oligonucleotide intensity values (beyond 1.5 deviations) are illustrated as individual spots.

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Use of Genomic DNA as an Indirect Reference for Identifying Gender-Associated Transcripts in Morphologically Identical, but Chromosomally Distinct, Schistosoma mansoni Cercariae

    doi: 10.1371/journal.pntd.0000323

    Figure Lengend Snippet: S. mansoni gDNA has superior hybridization characteristics compared to S. mansoni cDNA. The use of S. mansoni gDNA as a common reference reveals higher median intensity values and narrower overall intensity distributions than a complex S. mansoni cDNA reference. Box-plots display signal intensities for the AF-555 channel for S. japonicum , S. mansoni , M. musculus gDNA and complex reference S. mansoni cDNA pool (as described in Methods ). Boxes represent three independent experiments for mouse gDNA, S. mansoni gDNA and S. mansoni cDNA pool, respectively. S. japonicum gDNA is represented by a single experiment. All negative control microarray signals were removed before analysis, microarrays were filtered for manually excluded spots and each experiment was subsequently filtered to contain the same number of spots (n = 32,746). Statistical significance was defined using a Student's t-test between three independently replicated experiments. Horizontal lines represent median oligonucleotide intensity, boxes display oligonucleotide elements 25% above and below the median value and whiskers show oligonucleotide elements within 1.5 deviations of the median. Outlier oligonucleotide intensity values (beyond 1.5 deviations) are illustrated as individual spots.

    Article Snippet: BlueFuse for Microarrays (BlueGnome Ltd., UK) image analysis software was used to extract fluorescent signal intensity data.

    Techniques: Hybridization, Negative Control, Microarray

    Long-oligonucleotide DNA microarray is specific for S. mansoni nucleic acid material. S. mansoni gDNA hybridizes to the oligonucleotide DNA microarray with greater specificity and less variation compared to S. japonicum gDNA or a mixed pool of S. mansoni cDNA. Scatter plots display signal intensity for all oligonucleotides passing manual exclusion filters in all three displayed experiments. Correlation coefficient values for each comparison, R = 0.993, 0.956 and 0.350 indicate a high degree of correlation between AF555 and AF647 signal intensities from gDNA and cDNA, but not from S. mansoni AF555 labeled gDNA compared to S. japonicum AF647 labeled gDNA. A) Scatter plot for AF555 labeled S. mansoni gDNA compared to AF647 labeled S. mansoni gDNA signal intensities. B) Scatter plot for S. mansoni AF555 labeled cDNA compared to S. mansoni AF647 labeled cDNA (as described in Methods ) signal intensities. C) Scatter plot for S. mansoni AF555 labeled gDNA compared to S. japonicum AF647 labeled gDNA signal intensities. All negative control microarray signals were removed before analysis, microarrays were filtered for manually excluded spots and each experiment was subsequently filtered to contain the same number of spots (n = 34,220).

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Use of Genomic DNA as an Indirect Reference for Identifying Gender-Associated Transcripts in Morphologically Identical, but Chromosomally Distinct, Schistosoma mansoni Cercariae

    doi: 10.1371/journal.pntd.0000323

    Figure Lengend Snippet: Long-oligonucleotide DNA microarray is specific for S. mansoni nucleic acid material. S. mansoni gDNA hybridizes to the oligonucleotide DNA microarray with greater specificity and less variation compared to S. japonicum gDNA or a mixed pool of S. mansoni cDNA. Scatter plots display signal intensity for all oligonucleotides passing manual exclusion filters in all three displayed experiments. Correlation coefficient values for each comparison, R = 0.993, 0.956 and 0.350 indicate a high degree of correlation between AF555 and AF647 signal intensities from gDNA and cDNA, but not from S. mansoni AF555 labeled gDNA compared to S. japonicum AF647 labeled gDNA. A) Scatter plot for AF555 labeled S. mansoni gDNA compared to AF647 labeled S. mansoni gDNA signal intensities. B) Scatter plot for S. mansoni AF555 labeled cDNA compared to S. mansoni AF647 labeled cDNA (as described in Methods ) signal intensities. C) Scatter plot for S. mansoni AF555 labeled gDNA compared to S. japonicum AF647 labeled gDNA signal intensities. All negative control microarray signals were removed before analysis, microarrays were filtered for manually excluded spots and each experiment was subsequently filtered to contain the same number of spots (n = 34,220).

    Article Snippet: BlueFuse for Microarrays (BlueGnome Ltd., UK) image analysis software was used to extract fluorescent signal intensity data.

    Techniques: Microarray, Labeling, Negative Control

    Outline of the experimental approach used to identify 17 novel genes in F. diplosiphon that are responsive to changes in light color. Steps involved in the construction and analysis of genomic DNA microarrays, subarrays, Northern blots, and slot blots are shown.

    Journal: Journal of Bacteriology

    Article Title: Genomic DNA Microarray Analysis: Identification of New Genes Regulated by Light Color in the Cyanobacterium Fremyella diplosiphon

    doi: 10.1128/JB.186.13.4338-4349.2004

    Figure Lengend Snippet: Outline of the experimental approach used to identify 17 novel genes in F. diplosiphon that are responsive to changes in light color. Steps involved in the construction and analysis of genomic DNA microarrays, subarrays, Northern blots, and slot blots are shown.

    Article Snippet: The microarrays were printed on GAP slides (Corning Inc., Corning, N.Y.).

    Techniques: Northern Blot

    Altered epigenetic markers of the alpha-lactalbumin ( Lalba ) gene observed in BPA-exposed mammary glands. A. BPA-induced DNA demethylation near the Lalba promoter. p-values of the DNA methylation calculated from the microarray-based DNA methylation analysis are indicated. The PCR amplicon position for the ChIP-seq assay of H3K4me3 is shown as a red bar. B. ChIP assay of H3K4me3 at the Lalba transcription initiation site in the PND4 mammary glands. C. Quantitation following histone immunoprecipitation indicates enrichment of the Lalba promoter for the histone H3K4.

    Journal: PLoS ONE

    Article Title: Prenatal Exposure to BPA Alters the Epigenome of the Rat Mammary Gland and Increases the Propensity to Neoplastic Development

    doi: 10.1371/journal.pone.0099800

    Figure Lengend Snippet: Altered epigenetic markers of the alpha-lactalbumin ( Lalba ) gene observed in BPA-exposed mammary glands. A. BPA-induced DNA demethylation near the Lalba promoter. p-values of the DNA methylation calculated from the microarray-based DNA methylation analysis are indicated. The PCR amplicon position for the ChIP-seq assay of H3K4me3 is shown as a red bar. B. ChIP assay of H3K4me3 at the Lalba transcription initiation site in the PND4 mammary glands. C. Quantitation following histone immunoprecipitation indicates enrichment of the Lalba promoter for the histone H3K4.

    Article Snippet: Genomic DNA analysis In order to obtain sufficient material for microarray hybridization, 10 ng of IP and input gDNA from each sample were amplified using the GenomePlex Complete Whole Genome Amplification 2 (WGA2) kit (Sigma, St. Louis, MO).

    Techniques: DNA Methylation Assay, Microarray, Polymerase Chain Reaction, Amplification, Chromatin Immunoprecipitation, Quantitation Assay, Immunoprecipitation