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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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    77
    Agilent technologies microarray 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.
    Microarray Microarrays, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 77/100, based on 487 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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    95
    AutoGenomics microarrays
    Selectivity and sensitivity of carB -based oligonucleotide <t>microarray.</t>
    Microarrays, supplied by AutoGenomics, used in various techniques. Bioz Stars score: 95/100, based on 13 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 1558 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Kaneka Corp 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 Kaneka Corp, used in various techniques. Bioz Stars score: 91/100, based on 36 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 11456 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    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: 92/100, based on 94 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Bioarray 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 Bioarray, used in various techniques. Bioz Stars score: 94/100, based on 56 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    Thermo Fisher microarray hg u133a microarray
    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.
    Microarray Hg U133a Microarray, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 80/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    Biodiscovery LLC microarray hybridizations microarray slides
    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.
    Microarray Hybridizations Microarray Slides, supplied by Biodiscovery LLC, used in various techniques. Bioz Stars score: 80/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    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: 94/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    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: 92/100, 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: 90/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    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: 91/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    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: 97/100, based on 109 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    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: 91/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    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: 97/100, based on 724 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    98
    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: 98/100, based on 741 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Incyte 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 Incyte, used in various techniques. Bioz Stars score: 91/100, based on 38 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    NanoString Technologies Inc 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 NanoString Technologies Inc, used in various techniques. Bioz Stars score: 96/100, based on 52 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    LC Sciences 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 LC Sciences, used in various techniques. Bioz Stars score: 99/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    MOgene 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 MOgene, used in various techniques. Bioz Stars score: 96/100, based on 59 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Thermo Fisher microarray analysis a microarray
    ) 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.
    Microarray Analysis A Microarray, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 89/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Alere 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 Alere, used in various techniques. Bioz Stars score: 94/100, based on 69 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Alta Bioscience 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 Alta Bioscience, used in various techniques. Bioz Stars score: 90/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Thermo Fisher microarray data microarray data
    ) 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.
    Microarray Data Microarray Data, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    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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    77
    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: 77/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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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

    Dramatic improvement of Cy5 fluorescence stability as a result of ozone depletion. Pairs of microarrays printed in-house [A] or printed by Agilent Technologies [B] were hybridized and initially scanned immediately after washing in the carbon-filtered lab. One of each of the pairs of slides was then moved to an environment in which ozone was not removed by carbon filtration (ozone ~25 ppb for the in-house produced slide and ~10 ppb for the Agilent slide). The remaining slide remained in the ozone controlled microarray laboratory (ozone ~2–4 ppb). The slides were then alternately rescanned 6 times. The data show the rapid decline in Cy5 feature intensities as early as 13 minutes in the non-ozone controlled environment. It should be noted that the

    Journal: BMC Biotechnology

    Article Title: Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements

    doi: 10.1186/1472-6750-7-8

    Figure Lengend Snippet: Dramatic improvement of Cy5 fluorescence stability as a result of ozone depletion. Pairs of microarrays printed in-house [A] or printed by Agilent Technologies [B] were hybridized and initially scanned immediately after washing in the carbon-filtered lab. One of each of the pairs of slides was then moved to an environment in which ozone was not removed by carbon filtration (ozone ~25 ppb for the in-house produced slide and ~10 ppb for the Agilent slide). The remaining slide remained in the ozone controlled microarray laboratory (ozone ~2–4 ppb). The slides were then alternately rescanned 6 times. The data show the rapid decline in Cy5 feature intensities as early as 13 minutes in the non-ozone controlled environment. It should be noted that the "ozone-exposed" microarray was not exposed to ozone while it was being scanned.

    Article Snippet: Similar reductions in Cy5 intensities were also observed in Agilent microarrays (images not shown).

    Techniques: Fluorescence, Filtration, Produced, 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

    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

    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

    Separation of samples based on ordination multivariate analysis of microarray phylotype abundance data. Principal components analysis (PCA, A ) and unweighted (separation is based on phylotype presence, B ) and weighted (separation is based on phylotype presence and abundance, C ) principal coordinates analysis (PCoA) show separation of recipient samples before transplantation from both donor and recipient samples obtained after transplantation. Percent of dataset variability explained by each principal component/coordinate is shown in brackets in axis titles.

    Journal: Microbiome

    Article Title: Species and genus level resolution analysis of gut microbiota in Clostridium difficile patients following fecal microbiota transplantation

    doi: 10.1186/2049-2618-2-13

    Figure Lengend Snippet: Separation of samples based on ordination multivariate analysis of microarray phylotype abundance data. Principal components analysis (PCA, A ) and unweighted (separation is based on phylotype presence, B ) and weighted (separation is based on phylotype presence and abundance, C ) principal coordinates analysis (PCoA) show separation of recipient samples before transplantation from both donor and recipient samples obtained after transplantation. Percent of dataset variability explained by each principal component/coordinate is shown in brackets in axis titles.

    Article Snippet: The microarray data were corroborated with Illumina high-throughput sequencing and fluorescent in situ hybridization.

    Techniques: Microarray, Transplantation Assay

    Changes in microbiota diversity and composition following fecal transplantation in CDI patients. Microbiota communities were profiled from three CDI patients, healthy donor, and from each patient over a 4-month period following fecal transplantation. Samples were collected periodically as shown in (A) . Community diversity and evenness were assessed by calculating the Shannon H’ (diversity, B ) and Simpson E (evenness, C ) indices based on microarray phylotype abundance data. Community structure in each sample is shown at class level in (D) (distribution is based on microarray data) and (E) (distribution is based on sequencing data). Missing data represent samples that had lower amount of fecal material available; thus not all analyses could be carried out for these samples.

    Journal: Microbiome

    Article Title: Species and genus level resolution analysis of gut microbiota in Clostridium difficile patients following fecal microbiota transplantation

    doi: 10.1186/2049-2618-2-13

    Figure Lengend Snippet: Changes in microbiota diversity and composition following fecal transplantation in CDI patients. Microbiota communities were profiled from three CDI patients, healthy donor, and from each patient over a 4-month period following fecal transplantation. Samples were collected periodically as shown in (A) . Community diversity and evenness were assessed by calculating the Shannon H’ (diversity, B ) and Simpson E (evenness, C ) indices based on microarray phylotype abundance data. Community structure in each sample is shown at class level in (D) (distribution is based on microarray data) and (E) (distribution is based on sequencing data). Missing data represent samples that had lower amount of fecal material available; thus not all analyses could be carried out for these samples.

    Article Snippet: The microarray data were corroborated with Illumina high-throughput sequencing and fluorescent in situ hybridization.

    Techniques: Transplantation Assay, 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

    Chromosomal microarray showed a microduplication from 5q35.2 to 5q35.3(red box), arr[hg19] 5q35.2q35.3(176,062,669_179,524,425)×3, and corresponding region was displayed using the UCSC Genome Brower ( http://genome.ucsc.edu/ ). This region included 38 OMIM genes including FGFR4, NSD1, SLC34A1, F12, DOX41, B4GALT7, PROP1, NHP2, PHYKPL, GRM6, ADAMTS2, SQSTM1. LCR: low-copy repeats

    Journal: International Journal of Hematology-Oncology and Stem Cell Research

    Article Title: Unexplained Pancytopenia in a Patient with 5q35.2-q35.3 Microduplication Encompassing NSD1: A Case Report

    doi:

    Figure Lengend Snippet: Chromosomal microarray showed a microduplication from 5q35.2 to 5q35.3(red box), arr[hg19] 5q35.2q35.3(176,062,669_179,524,425)×3, and corresponding region was displayed using the UCSC Genome Brower ( http://genome.ucsc.edu/ ). This region included 38 OMIM genes including FGFR4, NSD1, SLC34A1, F12, DOX41, B4GALT7, PROP1, NHP2, PHYKPL, GRM6, ADAMTS2, SQSTM1. LCR: low-copy repeats

    Article Snippet: But the chromosomal microarray (Affymetrix CytoScan™ 750K Array) revealed a 3.46 Mb microduplication of 5q35.2-q35.3 region including NSD1 ( ).

    Techniques: Microarray

    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

    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

    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

    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

    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

    ) 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

    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