microarray slide Search Results


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  • 94
    Millipore microarray slides
    Carbohydrate <t>microarray</t> analyses of n-ArtinM ( A ) and y-ArtinM ( B ) . Numerical scores of the binding signals are means of duplicate spots at 7 fmol/spot (with error bars ). The complete list of probes and their sequences and binding scores are in Table 1 .
    Microarray Slides, supplied by Millipore, used in various techniques. Bioz Stars score: 94/100, based on 149 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Kaneka Corp microarray slides
    Validation of the 9 genes signature by qRT-PCR on 5 new PTC and 5 new ATC. The <t>microarray</t> expressions is also represented. Log 2 ratios represent the expression ratios of the genes in the tumors versus a pool of 23 normal thyroid tissues.
    Microarray Slides, supplied by Kaneka Corp, used in various techniques. Bioz Stars score: 92/100, based on 25 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Thermo Fisher microarray slides
    Validation of the 10 differentially expressed genes obtained from <t>microarray</t> analysis by qRT-PCR, n = 3. The p -values of the qRT-PCR data are as follows: 0.0067 (C6ORF52), 0.3920 (CCDC84), 0.3661 (THYMOSIN), 0.8195 (PRVE), 0.3154 (HSPCB), 0.6534 (CYP2J2), 0.002 (AMPD3), 0.1622 (TOR1AIP2), 0.8329 (PTGES3), 0.8808 (ACOX3).
    Microarray Slides, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 418 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Agilent technologies microarray slides
    Validation of <t>microarray</t> data by real-time qPCR . Mean (± SEM, n = 3) expression of the genes ef1alpha (housekeeping gene) , atoh1a , cdkn1b , JunB, gh1 , mlc1 , and myhc , as measured by microarray and qPCR. The expression profiles were similar between microarray and qPCR data.
    Microarray Slides, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 3664 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Roche microarray slides
    Expression profiles of the gene pac1 and the homologues of palC and palF genes in the <t>microarray</t> data. A) Expression of the genes in cultures of the strain QM9414 at pH 3, 4.5 and 6. B) Expression of the genes in cultures of the Δ pac1 strain and in QM9414 at pH 6. Expression level of the genes is the normalised signal in the microarray data (not log2 transformed values), data on the three biological replicates is averaged. The time point and pH of the culture, as well as the strain, is indicated in the X axis labels. QM is an abbreviation for QM9414.
    Microarray Slides, supplied by Roche, used in various techniques. Bioz Stars score: 93/100, based on 117 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Agilent technologies microarray slide
    LGP2 regulates miRNA-mediated gene expression of endogenous genes in human cells. ( A ) XY plot of <t>microarray</t> signals of all transcripts expressed in WT and LGP2 −/− cells. ( B ) MA plots (above) and cumulative distributions (below) of all transcripts in LGP2 −/− cells normalized by their expression levels in WT cells. The predicted targets of miR-106b (left) and miR-19b-1 (right) are colored blue and pink, respectively. ZNFX1 and DERL2 are the predicted targets of miR-106b, but not miR-19b-1. ( C ) The differences of integral values of cumulative distribution between all transcripts and predicted targets were calculated on all of the predicted targets of each TRBP-bound pre-miRNA (sequence read enrichment by immunoprecipitation > 10) and TRBP-non-bound pre-miRNA (sequence read enrichment by immunoprecipitation
    Microarray Slide, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 614 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Corning Life Sciences microarray slides
    Volcano plot of M. sedula <t>microarray</t> dye-flip results (YE versus YE+FeSO 4 ). Negative x -axis values represent ORFs more highly transcribed on YE+FeSO 4 while positive x -axis values represent ORFs more highly transcribed on YE alone. As points
    Microarray Slides, supplied by Corning Life Sciences, used in various techniques. Bioz Stars score: 92/100, based on 97 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Corning Life Sciences microarray slide
    Threshold sensitivity of the DNA oligonucleotide array. Genomic DNA from various concentrations of C. jejuni strain NCTC11168 cells were isolated, CyDye labeled, and hybridized to the <t>microarray.</t> The average fluorescence signal for each C. jejuni probe
    Microarray Slide, supplied by Corning Life Sciences, used in various techniques. Bioz Stars score: 91/100, based on 91 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    MWG-Biotech slide microarrays
    Threshold sensitivity of the DNA oligonucleotide array. Genomic DNA from various concentrations of C. jejuni strain NCTC11168 cells were isolated, CyDye labeled, and hybridized to the <t>microarray.</t> The average fluorescence signal for each C. jejuni probe
    Slide Microarrays, supplied by MWG-Biotech, used in various techniques. Bioz Stars score: 88/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    CombiMatrix microarray slide
    Venn diagrams showing numbers of barley genes shown by the <t>microarray</t> analysis to be significantly induced (A) or repressed (B) in barley embryos after inoculation with P. graminea for various combinations of genotypes and time‐points. The genotypes are Mirco‐ rdg2a (M‐ rdg2a ) and NIL3876‐ Rdg2a (NIL‐ Rdg2a ), and the time points are 7 and 14 dai. For each individual genotype/time‐point combination, the total number of induced/repressed genes is shown in parentheses.
    Microarray Slide, supplied by CombiMatrix, used in various techniques. Bioz Stars score: 91/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Full Moon BioSystems microarray slides
    Three types of spot morphology in a real <t>microarray</t> image . (A) The doughnut-shaped spot. (B) The peak-shaped spot. (C) The volcano-shaped spot.
    Microarray Slides, supplied by Full Moon BioSystems, used in various techniques. Bioz Stars score: 92/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Genisphere microarray slide
    Three types of spot morphology in a real <t>microarray</t> image . (A) The doughnut-shaped spot. (B) The peak-shaped spot. (C) The volcano-shaped spot.
    Microarray Slide, supplied by Genisphere, used in various techniques. Bioz Stars score: 91/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Biodiscovery LLC microarray hybridizations microarray slides
    Three types of spot morphology in a real <t>microarray</t> image . (A) The doughnut-shaped spot. (B) The peak-shaped spot. (C) The volcano-shaped spot.
    Microarray Hybridizations Microarray Slides, supplied by Biodiscovery LLC, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Agilent technologies v19 microarray slides
    Three types of spot morphology in a real <t>microarray</t> image . (A) The doughnut-shaped spot. (B) The peak-shaped spot. (C) The volcano-shaped spot.
    V19 Microarray Slides, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Agilent technologies 44k microarray slide
    Three types of spot morphology in a real <t>microarray</t> image . (A) The doughnut-shaped spot. (B) The peak-shaped spot. (C) The volcano-shaped spot.
    44k Microarray Slide, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 85/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Agilent technologies 60k microarray slides
    Three types of spot morphology in a real <t>microarray</t> image . (A) The doughnut-shaped spot. (B) The peak-shaped spot. (C) The volcano-shaped spot.
    60k Microarray Slides, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 90/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Roche plex microarray slides
    Transcriptional profiling data comparing the production strategies. (A) Volcano plots of the combined triplicate RNA <t>microarray</t> data at the points of highest interest, 22 and 27 hours showing the spread of gene expression events in terms of up and down regulation between each production strategy comparison. (B) A table showing the transcriptional changes exceeding the 2-fold change threshold for each comparison and also listed by gene category throughout the cultivations. The total number of hits shows the combined number of transcriptional changes for all of the production strategies and the final column shows the mutual transcriptional changes observed between secretion and intracellular production. In the case of intracellular production most of these transcriptional changes observed are also found in the mutual category showing that many similar genes are highlighted between both types of production.
    Plex Microarray Slides, supplied by Roche, used in various techniques. Bioz Stars score: 86/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Millipore sigmascreen microarray slides
    Transcriptional profiling data comparing the production strategies. (A) Volcano plots of the combined triplicate RNA <t>microarray</t> data at the points of highest interest, 22 and 27 hours showing the spread of gene expression events in terms of up and down regulation between each production strategy comparison. (B) A table showing the transcriptional changes exceeding the 2-fold change threshold for each comparison and also listed by gene category throughout the cultivations. The total number of hits shows the combined number of transcriptional changes for all of the production strategies and the final column shows the mutual transcriptional changes observed between secretion and intracellular production. In the case of intracellular production most of these transcriptional changes observed are also found in the mutual category showing that many similar genes are highlighted between both types of production.
    Sigmascreen Microarray Slides, supplied by Millipore, used in various techniques. Bioz Stars score: 85/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    SurModics codelink microarray slides
    Transcriptional profiling data comparing the production strategies. (A) Volcano plots of the combined triplicate RNA <t>microarray</t> data at the points of highest interest, 22 and 27 hours showing the spread of gene expression events in terms of up and down regulation between each production strategy comparison. (B) A table showing the transcriptional changes exceeding the 2-fold change threshold for each comparison and also listed by gene category throughout the cultivations. The total number of hits shows the combined number of transcriptional changes for all of the production strategies and the final column shows the mutual transcriptional changes observed between secretion and intracellular production. In the case of intracellular production most of these transcriptional changes observed are also found in the mutual category showing that many similar genes are highlighted between both types of production.
    Codelink Microarray Slides, supplied by SurModics, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Agilent technologies microarray gasket slide
    Transcriptomic response of S. pombe as a function of changes in iron levels and effect of php4 ∆ /php4 ∆ disruption relative to wild-type cells during meiotic differentiation. (A) Cultures of pat1-114/pat1-114 php4 + /php4 + cells were precultivated in the presence of Fe (0.74 µM) and Dip (50 µM) for 16 hr. Pretreated cells were further exposed to Fe (100 µM) and Dip (75 µM), respectively, and then immediately induced to undergo synchronous meiosis. After 7 hr of meiotic induction, total RNA was extracted and used for <t>microarray</t> experiments. The graph represents a genome-wide picture of differentially expressed genes (X axis) in iron-replete vs. iron-limited cells. For simplicity, only a few differentially expressed transcripts are labeled on the graph. (B) Genome-wide picture of differentially expressed genes in pat1-114/pat1-114 php4 Δ /php4 Δ vs. pat1-114/pat1-114 php4 + /php4 + cells that had been precultured (50 µM) and cultured (75 µM) in the presence of Dip. Genome-wide transcripts (X axis) were analyzed by DNA microarrays. All differentially expressed genes are depicted, although only a few of them are labeled on the graph for the sake of clarity. (C) Venn diagram representing the number of genes that were induced in iron-treated php4 + /php4 + cells compared to php4 + /php4 + cells grown under iron-limiting conditions and the number of genes that exhibited higher expression levels in iron-starved php4 ∆/ php4 ∆ compared to php4 + /php4 + cells grown under the same conditions. Dip, 2,2’-dipyridyl; Fe, iron(III) chloride.
    Microarray Gasket Slide, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 90/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Corning Life Sciences ultragap microarray slides
    Transcriptomic response of S. pombe as a function of changes in iron levels and effect of php4 ∆ /php4 ∆ disruption relative to wild-type cells during meiotic differentiation. (A) Cultures of pat1-114/pat1-114 php4 + /php4 + cells were precultivated in the presence of Fe (0.74 µM) and Dip (50 µM) for 16 hr. Pretreated cells were further exposed to Fe (100 µM) and Dip (75 µM), respectively, and then immediately induced to undergo synchronous meiosis. After 7 hr of meiotic induction, total RNA was extracted and used for <t>microarray</t> experiments. The graph represents a genome-wide picture of differentially expressed genes (X axis) in iron-replete vs. iron-limited cells. For simplicity, only a few differentially expressed transcripts are labeled on the graph. (B) Genome-wide picture of differentially expressed genes in pat1-114/pat1-114 php4 Δ /php4 Δ vs. pat1-114/pat1-114 php4 + /php4 + cells that had been precultured (50 µM) and cultured (75 µM) in the presence of Dip. Genome-wide transcripts (X axis) were analyzed by DNA microarrays. All differentially expressed genes are depicted, although only a few of them are labeled on the graph for the sake of clarity. (C) Venn diagram representing the number of genes that were induced in iron-treated php4 + /php4 + cells compared to php4 + /php4 + cells grown under iron-limiting conditions and the number of genes that exhibited higher expression levels in iron-starved php4 ∆/ php4 ∆ compared to php4 + /php4 + cells grown under the same conditions. Dip, 2,2’-dipyridyl; Fe, iron(III) chloride.
    Ultragap Microarray Slides, supplied by Corning Life Sciences, used in various techniques. Bioz Stars score: 85/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    OakLabs microarray slide hybridization
    Summary of <t>microarray</t> analysis of two different rice varieties, MTU9 (sensitive) and SML242 (tolerant) in response to B stress treatment. Data are from experiment Btox3. Differentially expressed genes (DEGs) are shown in red.
    Microarray Slide Hybridization, supplied by OakLabs, used in various techniques. Bioz Stars score: 91/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Carbohydrate microarray analyses of n-ArtinM ( A ) and y-ArtinM ( B ) . Numerical scores of the binding signals are means of duplicate spots at 7 fmol/spot (with error bars ). The complete list of probes and their sequences and binding scores are in Table 1 .

    Journal: Data in Brief

    Article Title: Glycan microarray analysis of the carbohydrate-recognition specificity of native and recombinant forms of the lectin ArtinM

    doi: 10.1016/j.dib.2015.11.014

    Figure Lengend Snippet: Carbohydrate microarray analyses of n-ArtinM ( A ) and y-ArtinM ( B ) . Numerical scores of the binding signals are means of duplicate spots at 7 fmol/spot (with error bars ). The complete list of probes and their sequences and binding scores are in Table 1 .

    Article Snippet: In brief, microarray slides were blocked at ambient temperature with 1% w/v bovine serum albumin (BSA; Sigma-Aldrich) in casein blocker solution (Pierce Chemical Co, USA) for 1 h. The biotinylated lectin samples were overlaid at 50 μg/mL, and binding was detected using Alexa Fluor 647-labeled streptavidin (Molecular Probes-Life Technologies, CA, USA) at 1 μg/mL in blocker solution.

    Techniques: Microarray, Binding Assay

    Validation of the 9 genes signature by qRT-PCR on 5 new PTC and 5 new ATC. The microarray expressions is also represented. Log 2 ratios represent the expression ratios of the genes in the tumors versus a pool of 23 normal thyroid tissues.

    Journal: PLoS ONE

    Article Title: mRNA Expression in Papillary and Anaplastic Thyroid Carcinoma: Molecular Anatomy of a Killing Switch

    doi: 10.1371/journal.pone.0037807

    Figure Lengend Snippet: Validation of the 9 genes signature by qRT-PCR on 5 new PTC and 5 new ATC. The microarray expressions is also represented. Log 2 ratios represent the expression ratios of the genes in the tumors versus a pool of 23 normal thyroid tissues.

    Article Snippet: Validation of Microarray Results by Quantitative Real-time RT-PCR (qRT-PCR) A number of modulated genes on the microarray slides were validated using qRT-PCR (SYBR Green, Eurogentec, Liege, Belgium).

    Techniques: Quantitative RT-PCR, Microarray, Expressing

    Validation of the 10 differentially expressed genes obtained from microarray analysis by qRT-PCR, n = 3. The p -values of the qRT-PCR data are as follows: 0.0067 (C6ORF52), 0.3920 (CCDC84), 0.3661 (THYMOSIN), 0.8195 (PRVE), 0.3154 (HSPCB), 0.6534 (CYP2J2), 0.002 (AMPD3), 0.1622 (TOR1AIP2), 0.8329 (PTGES3), 0.8808 (ACOX3).

    Journal: PLoS ONE

    Article Title: Genome-Wide Gene Expression Profiles in Lung Tissues of Pig Breeds Differing in Resistance to Porcine Reproductive and Respiratory Syndrome Virus

    doi: 10.1371/journal.pone.0086101

    Figure Lengend Snippet: Validation of the 10 differentially expressed genes obtained from microarray analysis by qRT-PCR, n = 3. The p -values of the qRT-PCR data are as follows: 0.0067 (C6ORF52), 0.3920 (CCDC84), 0.3661 (THYMOSIN), 0.8195 (PRVE), 0.3154 (HSPCB), 0.6534 (CYP2J2), 0.002 (AMPD3), 0.1622 (TOR1AIP2), 0.8329 (PTGES3), 0.8808 (ACOX3).

    Article Snippet: After hybridization, the microarray slides were washed and dyed with the Affymetrix Fluidics Station 450.

    Techniques: Microarray, Quantitative RT-PCR

    Validation of microarray data by real-time qPCR . Mean (± SEM, n = 3) expression of the genes ef1alpha (housekeeping gene) , atoh1a , cdkn1b , JunB, gh1 , mlc1 , and myhc , as measured by microarray and qPCR. The expression profiles were similar between microarray and qPCR data.

    Journal: BMC Neuroscience

    Article Title: Transcriptomic analysis of the zebrafish inner ear points to growth hormone mediated regeneration following acoustic trauma

    doi: 10.1186/1471-2202-12-88

    Figure Lengend Snippet: Validation of microarray data by real-time qPCR . Mean (± SEM, n = 3) expression of the genes ef1alpha (housekeeping gene) , atoh1a , cdkn1b , JunB, gh1 , mlc1 , and myhc , as measured by microarray and qPCR. The expression profiles were similar between microarray and qPCR data.

    Article Snippet: After hybridization, the microarray slides were washed with Agilent gene expression wash buffers.

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

    Canonical pathway analysis reveals growth hormone-related gene regulation . Canonical pathway analysis showing known growth-hormone related pathways. Red-colored genes are up-regulated and gray-colored genes are down-regulated in the zebrafish microarray data set at two days following acoustic trauma. Numbers below genes represent fold changes and P -values.

    Journal: BMC Neuroscience

    Article Title: Transcriptomic analysis of the zebrafish inner ear points to growth hormone mediated regeneration following acoustic trauma

    doi: 10.1186/1471-2202-12-88

    Figure Lengend Snippet: Canonical pathway analysis reveals growth hormone-related gene regulation . Canonical pathway analysis showing known growth-hormone related pathways. Red-colored genes are up-regulated and gray-colored genes are down-regulated in the zebrafish microarray data set at two days following acoustic trauma. Numbers below genes represent fold changes and P -values.

    Article Snippet: After hybridization, the microarray slides were washed with Agilent gene expression wash buffers.

    Techniques: Microarray

    Volcano plots and heat maps showing the time course of acoustic trauma-related differential gene expression in the zebrafish inner ear . RNA samples from zebrafish inner ears of controls or subjects exposed to acoustic trauma and allowed to recover for either two or four days and then hybridized to a zebrafish microarray, which measures expression (mRNA abundance) for 21,000 gene transcipts. Volcano plots show differential gene expression between (A) controls and two days post-trauma (D2), (B) controls and four days post-trauma (D4), and (C) two versus four days post-trauma. The Y-axes of the volcano plots display the negative log (base 10) of P values from paired t -tests, while the X-axes show the log (base 2) of the fold differences between the groups. The horizontal line represents the P = 0.05 value, and the vertical lines corresponding to fold differences of 1.4 and -1.4, respectively. Genes with paired t-test P

    Journal: BMC Neuroscience

    Article Title: Transcriptomic analysis of the zebrafish inner ear points to growth hormone mediated regeneration following acoustic trauma

    doi: 10.1186/1471-2202-12-88

    Figure Lengend Snippet: Volcano plots and heat maps showing the time course of acoustic trauma-related differential gene expression in the zebrafish inner ear . RNA samples from zebrafish inner ears of controls or subjects exposed to acoustic trauma and allowed to recover for either two or four days and then hybridized to a zebrafish microarray, which measures expression (mRNA abundance) for 21,000 gene transcipts. Volcano plots show differential gene expression between (A) controls and two days post-trauma (D2), (B) controls and four days post-trauma (D4), and (C) two versus four days post-trauma. The Y-axes of the volcano plots display the negative log (base 10) of P values from paired t -tests, while the X-axes show the log (base 2) of the fold differences between the groups. The horizontal line represents the P = 0.05 value, and the vertical lines corresponding to fold differences of 1.4 and -1.4, respectively. Genes with paired t-test P

    Article Snippet: After hybridization, the microarray slides were washed with Agilent gene expression wash buffers.

    Techniques: Expressing, Microarray

    Expression profiles of the gene pac1 and the homologues of palC and palF genes in the microarray data. A) Expression of the genes in cultures of the strain QM9414 at pH 3, 4.5 and 6. B) Expression of the genes in cultures of the Δ pac1 strain and in QM9414 at pH 6. Expression level of the genes is the normalised signal in the microarray data (not log2 transformed values), data on the three biological replicates is averaged. The time point and pH of the culture, as well as the strain, is indicated in the X axis labels. QM is an abbreviation for QM9414.

    Journal: Microbial Cell Factories

    Article Title: The effects of extracellular pH and of the transcriptional regulator PACI on the transcriptome of Trichoderma reesei

    doi: 10.1186/s12934-015-0247-z

    Figure Lengend Snippet: Expression profiles of the gene pac1 and the homologues of palC and palF genes in the microarray data. A) Expression of the genes in cultures of the strain QM9414 at pH 3, 4.5 and 6. B) Expression of the genes in cultures of the Δ pac1 strain and in QM9414 at pH 6. Expression level of the genes is the normalised signal in the microarray data (not log2 transformed values), data on the three biological replicates is averaged. The time point and pH of the culture, as well as the strain, is indicated in the X axis labels. QM is an abbreviation for QM9414.

    Article Snippet: The probe design and manufacturing of the microarray slides was carried out by RocheNimbleGen using an array design based on the T. reesei genome version 2.0 [ ].

    Techniques: Expressing, Microarray, Transformation Assay

    LGP2 regulates miRNA-mediated gene expression of endogenous genes in human cells. ( A ) XY plot of microarray signals of all transcripts expressed in WT and LGP2 −/− cells. ( B ) MA plots (above) and cumulative distributions (below) of all transcripts in LGP2 −/− cells normalized by their expression levels in WT cells. The predicted targets of miR-106b (left) and miR-19b-1 (right) are colored blue and pink, respectively. ZNFX1 and DERL2 are the predicted targets of miR-106b, but not miR-19b-1. ( C ) The differences of integral values of cumulative distribution between all transcripts and predicted targets were calculated on all of the predicted targets of each TRBP-bound pre-miRNA (sequence read enrichment by immunoprecipitation > 10) and TRBP-non-bound pre-miRNA (sequence read enrichment by immunoprecipitation

    Journal: Nucleic Acids Research

    Article Title: LGP2 virus sensor regulates gene expression network mediated by TRBP-bound microRNAs

    doi: 10.1093/nar/gky575

    Figure Lengend Snippet: LGP2 regulates miRNA-mediated gene expression of endogenous genes in human cells. ( A ) XY plot of microarray signals of all transcripts expressed in WT and LGP2 −/− cells. ( B ) MA plots (above) and cumulative distributions (below) of all transcripts in LGP2 −/− cells normalized by their expression levels in WT cells. The predicted targets of miR-106b (left) and miR-19b-1 (right) are colored blue and pink, respectively. ZNFX1 and DERL2 are the predicted targets of miR-106b, but not miR-19b-1. ( C ) The differences of integral values of cumulative distribution between all transcripts and predicted targets were calculated on all of the predicted targets of each TRBP-bound pre-miRNA (sequence read enrichment by immunoprecipitation > 10) and TRBP-non-bound pre-miRNA (sequence read enrichment by immunoprecipitation

    Article Snippet: Cy-3 labeled RNAs were fragmented by Gene Expression Hybridization kit (Agilent Technologies) and hybridized to SurePrint G3 Human GE microarray version 3 (Agilent Technologies) at 65°C for 17 h. After being washed, microarray slide was scanned by DNA Microarray Scanner (Agilent Technologies) and quantified signals by Feature Extraction 10.5.1.1 (Agilent Technologies).

    Techniques: Expressing, Microarray, Sequencing, Immunoprecipitation

    Volcano plot of M. sedula microarray dye-flip results (YE versus YE+FeSO 4 ). Negative x -axis values represent ORFs more highly transcribed on YE+FeSO 4 while positive x -axis values represent ORFs more highly transcribed on YE alone. As points

    Journal: Applied and Environmental Microbiology

    Article Title: The Genome Sequence of the Metal-Mobilizing, Extremely Thermoacidophilic Archaeon Metallosphaera sedula Provides Insights into Bioleaching-Associated Metabolism ▿ Provides Insights into Bioleaching-Associated Metabolism ▿ †

    doi: 10.1128/AEM.02019-07

    Figure Lengend Snippet: Volcano plot of M. sedula microarray dye-flip results (YE versus YE+FeSO 4 ). Negative x -axis values represent ORFs more highly transcribed on YE+FeSO 4 while positive x -axis values represent ORFs more highly transcribed on YE alone. As points

    Article Snippet: RNA was extracted and purified (RNAqueous; Ambion), reverse transcribed (Superscript III, Invitrogen), repurified, labeled with either Cy3 or Cy5 dye (GE Healthcare), and hybridized to one of two microarray slides (Corning).

    Techniques: Microarray

    Threshold sensitivity of the DNA oligonucleotide array. Genomic DNA from various concentrations of C. jejuni strain NCTC11168 cells were isolated, CyDye labeled, and hybridized to the microarray. The average fluorescence signal for each C. jejuni probe

    Journal: Applied and Environmental Microbiology

    Article Title: Detection and Genotyping of Arcobacter and Campylobacter Isolates from Retail Chicken Samples by Use of DNA Oligonucleotide Arrays ▿ Isolates from Retail Chicken Samples by Use of DNA Oligonucleotide Arrays ▿ †

    doi: 10.1128/AEM.02984-06

    Figure Lengend Snippet: Threshold sensitivity of the DNA oligonucleotide array. Genomic DNA from various concentrations of C. jejuni strain NCTC11168 cells were isolated, CyDye labeled, and hybridized to the microarray. The average fluorescence signal for each C. jejuni probe

    Article Snippet: The microarray slide was placed in a hybridization chamber (Corning) and was incubated at 42°C for 18 h, as in previous studies ( ).

    Techniques: Isolation, Labeling, Microarray, Fluorescence

    Validation of the DNA oligonucleotide array for identifying pathogens in food. (A) Genomic DNA from bacterial isolates recovered from a 24-h enrichment broth was labeled with CyDye and hybridized to the microarray. The average fluorescence signal for

    Journal: Applied and Environmental Microbiology

    Article Title: Detection and Genotyping of Arcobacter and Campylobacter Isolates from Retail Chicken Samples by Use of DNA Oligonucleotide Arrays ▿ Isolates from Retail Chicken Samples by Use of DNA Oligonucleotide Arrays ▿ †

    doi: 10.1128/AEM.02984-06

    Figure Lengend Snippet: Validation of the DNA oligonucleotide array for identifying pathogens in food. (A) Genomic DNA from bacterial isolates recovered from a 24-h enrichment broth was labeled with CyDye and hybridized to the microarray. The average fluorescence signal for

    Article Snippet: The microarray slide was placed in a hybridization chamber (Corning) and was incubated at 42°C for 18 h, as in previous studies ( ).

    Techniques: Labeling, Microarray, Fluorescence

    Probe specificity of the DNA oligonucleotide array. Genomic DNA from A. butzleri ( Ab ), A. cryaerophilus ( Ac ), C. coli ( Cc ), and C. jejuni ( Cj ) reference strains (Table ) was labeled separately with CyDye and hybridized to the microarray.

    Journal: Applied and Environmental Microbiology

    Article Title: Detection and Genotyping of Arcobacter and Campylobacter Isolates from Retail Chicken Samples by Use of DNA Oligonucleotide Arrays ▿ Isolates from Retail Chicken Samples by Use of DNA Oligonucleotide Arrays ▿ †

    doi: 10.1128/AEM.02984-06

    Figure Lengend Snippet: Probe specificity of the DNA oligonucleotide array. Genomic DNA from A. butzleri ( Ab ), A. cryaerophilus ( Ac ), C. coli ( Cc ), and C. jejuni ( Cj ) reference strains (Table ) was labeled separately with CyDye and hybridized to the microarray.

    Article Snippet: The microarray slide was placed in a hybridization chamber (Corning) and was incubated at 42°C for 18 h, as in previous studies ( ).

    Techniques: Labeling, Microarray

    Multiplex PCR for species identification of Arcobacter ) was performed to validate the microarray data for species identification of Arcobacter isolates from retail chicken samples as determined by microarray analysis.

    Journal: Applied and Environmental Microbiology

    Article Title: Detection and Genotyping of Arcobacter and Campylobacter Isolates from Retail Chicken Samples by Use of DNA Oligonucleotide Arrays ▿ Isolates from Retail Chicken Samples by Use of DNA Oligonucleotide Arrays ▿ †

    doi: 10.1128/AEM.02984-06

    Figure Lengend Snippet: Multiplex PCR for species identification of Arcobacter ) was performed to validate the microarray data for species identification of Arcobacter isolates from retail chicken samples as determined by microarray analysis.

    Article Snippet: The microarray slide was placed in a hybridization chamber (Corning) and was incubated at 42°C for 18 h, as in previous studies ( ).

    Techniques: Multiplex Assay, Polymerase Chain Reaction, Microarray

    Venn diagrams showing numbers of barley genes shown by the microarray analysis to be significantly induced (A) or repressed (B) in barley embryos after inoculation with P. graminea for various combinations of genotypes and time‐points. The genotypes are Mirco‐ rdg2a (M‐ rdg2a ) and NIL3876‐ Rdg2a (NIL‐ Rdg2a ), and the time points are 7 and 14 dai. For each individual genotype/time‐point combination, the total number of induced/repressed genes is shown in parentheses.

    Journal: Molecular Plant Pathology

    Article Title: Histological and molecular analysis of Rdg2a barley resistance to leaf stripe

    doi: 10.1111/j.1364-3703.2008.00479.x

    Figure Lengend Snippet: Venn diagrams showing numbers of barley genes shown by the microarray analysis to be significantly induced (A) or repressed (B) in barley embryos after inoculation with P. graminea for various combinations of genotypes and time‐points. The genotypes are Mirco‐ rdg2a (M‐ rdg2a ) and NIL3876‐ Rdg2a (NIL‐ Rdg2a ), and the time points are 7 and 14 dai. For each individual genotype/time‐point combination, the total number of induced/repressed genes is shown in parentheses.

    Article Snippet: A total of 2240 35–40 mer probes were synthesized onto each sector of a CustomArray 4 × 2000 microarray slide (CombiMatrix Corp., WA).

    Techniques: Microarray

    Three types of spot morphology in a real microarray image . (A) The doughnut-shaped spot. (B) The peak-shaped spot. (C) The volcano-shaped spot.

    Journal: BMC Bioinformatics

    Article Title: Characterization and simulation of cDNA microarray spots using a novel mathematical model

    doi: 10.1186/1471-2105-8-485

    Figure Lengend Snippet: Three types of spot morphology in a real microarray image . (A) The doughnut-shaped spot. (B) The peak-shaped spot. (C) The volcano-shaped spot.

    Article Snippet: While homemade poly-L-lysine-coated glass slides have been widely used, several commercial microarray slides are now preferred, such as the FMB cDNA slide (Full Moon Biosystems Inc.), ArrayIt SuperAmine and SuperAldehyde slides (TeleChem International, Inc.).

    Techniques: Microarray

    Various spot shapes in real microarray images . (A) Real microarray images contain spots in various shapes [38] [40]. (B) The 3D image of spots in the real microarray images were reconstructed by plotting image intensity on the z-axis (C) The radial profiles of the 3D images were obtained where the section passed through the centre.

    Journal: BMC Bioinformatics

    Article Title: Characterization and simulation of cDNA microarray spots using a novel mathematical model

    doi: 10.1186/1471-2105-8-485

    Figure Lengend Snippet: Various spot shapes in real microarray images . (A) Real microarray images contain spots in various shapes [38] [40]. (B) The 3D image of spots in the real microarray images were reconstructed by plotting image intensity on the z-axis (C) The radial profiles of the 3D images were obtained where the section passed through the centre.

    Article Snippet: While homemade poly-L-lysine-coated glass slides have been widely used, several commercial microarray slides are now preferred, such as the FMB cDNA slide (Full Moon Biosystems Inc.), ArrayIt SuperAmine and SuperAldehyde slides (TeleChem International, Inc.).

    Techniques: Microarray

    Transcriptional profiling data comparing the production strategies. (A) Volcano plots of the combined triplicate RNA microarray data at the points of highest interest, 22 and 27 hours showing the spread of gene expression events in terms of up and down regulation between each production strategy comparison. (B) A table showing the transcriptional changes exceeding the 2-fold change threshold for each comparison and also listed by gene category throughout the cultivations. The total number of hits shows the combined number of transcriptional changes for all of the production strategies and the final column shows the mutual transcriptional changes observed between secretion and intracellular production. In the case of intracellular production most of these transcriptional changes observed are also found in the mutual category showing that many similar genes are highlighted between both types of production.

    Journal: BMC Biotechnology

    Article Title: Comparison of intracellular and secretion-based strategies for production of human α-galactosidase A in the filamentous fungus Trichoderma reesei

    doi: 10.1186/s12896-014-0091-y

    Figure Lengend Snippet: Transcriptional profiling data comparing the production strategies. (A) Volcano plots of the combined triplicate RNA microarray data at the points of highest interest, 22 and 27 hours showing the spread of gene expression events in terms of up and down regulation between each production strategy comparison. (B) A table showing the transcriptional changes exceeding the 2-fold change threshold for each comparison and also listed by gene category throughout the cultivations. The total number of hits shows the combined number of transcriptional changes for all of the production strategies and the final column shows the mutual transcriptional changes observed between secretion and intracellular production. In the case of intracellular production most of these transcriptional changes observed are also found in the mutual category showing that many similar genes are highlighted between both types of production.

    Article Snippet: The labelled cDNA was hybridised on an automated HS12 system (Roche) to custom-made four plex microarray slides (Roche) designed from the T. reesei genome version 2.0 [ , ].

    Techniques: Microarray, Expressing

    Transcriptomic response of S. pombe as a function of changes in iron levels and effect of php4 ∆ /php4 ∆ disruption relative to wild-type cells during meiotic differentiation. (A) Cultures of pat1-114/pat1-114 php4 + /php4 + cells were precultivated in the presence of Fe (0.74 µM) and Dip (50 µM) for 16 hr. Pretreated cells were further exposed to Fe (100 µM) and Dip (75 µM), respectively, and then immediately induced to undergo synchronous meiosis. After 7 hr of meiotic induction, total RNA was extracted and used for microarray experiments. The graph represents a genome-wide picture of differentially expressed genes (X axis) in iron-replete vs. iron-limited cells. For simplicity, only a few differentially expressed transcripts are labeled on the graph. (B) Genome-wide picture of differentially expressed genes in pat1-114/pat1-114 php4 Δ /php4 Δ vs. pat1-114/pat1-114 php4 + /php4 + cells that had been precultured (50 µM) and cultured (75 µM) in the presence of Dip. Genome-wide transcripts (X axis) were analyzed by DNA microarrays. All differentially expressed genes are depicted, although only a few of them are labeled on the graph for the sake of clarity. (C) Venn diagram representing the number of genes that were induced in iron-treated php4 + /php4 + cells compared to php4 + /php4 + cells grown under iron-limiting conditions and the number of genes that exhibited higher expression levels in iron-starved php4 ∆/ php4 ∆ compared to php4 + /php4 + cells grown under the same conditions. Dip, 2,2’-dipyridyl; Fe, iron(III) chloride.

    Journal: G3: Genes|Genomes|Genetics

    Article Title: Php4 Is a Key Player for Iron Economy in Meiotic and Sporulating Cells

    doi: 10.1534/g3.116.031898

    Figure Lengend Snippet: Transcriptomic response of S. pombe as a function of changes in iron levels and effect of php4 ∆ /php4 ∆ disruption relative to wild-type cells during meiotic differentiation. (A) Cultures of pat1-114/pat1-114 php4 + /php4 + cells were precultivated in the presence of Fe (0.74 µM) and Dip (50 µM) for 16 hr. Pretreated cells were further exposed to Fe (100 µM) and Dip (75 µM), respectively, and then immediately induced to undergo synchronous meiosis. After 7 hr of meiotic induction, total RNA was extracted and used for microarray experiments. The graph represents a genome-wide picture of differentially expressed genes (X axis) in iron-replete vs. iron-limited cells. For simplicity, only a few differentially expressed transcripts are labeled on the graph. (B) Genome-wide picture of differentially expressed genes in pat1-114/pat1-114 php4 Δ /php4 Δ vs. pat1-114/pat1-114 php4 + /php4 + cells that had been precultured (50 µM) and cultured (75 µM) in the presence of Dip. Genome-wide transcripts (X axis) were analyzed by DNA microarrays. All differentially expressed genes are depicted, although only a few of them are labeled on the graph for the sake of clarity. (C) Venn diagram representing the number of genes that were induced in iron-treated php4 + /php4 + cells compared to php4 + /php4 + cells grown under iron-limiting conditions and the number of genes that exhibited higher expression levels in iron-starved php4 ∆/ php4 ∆ compared to php4 + /php4 + cells grown under the same conditions. Dip, 2,2’-dipyridyl; Fe, iron(III) chloride.

    Article Snippet: First, the microarray gasket slide from Agilent Technologies was improved in that it contained a larger number of probes (15,000) which allowed a ∼2–3 × increased coverage for each S. pombe ORF.

    Techniques: Microarray, Genome Wide, Labeling, Cell Culture, Expressing

    Summary of microarray analysis of two different rice varieties, MTU9 (sensitive) and SML242 (tolerant) in response to B stress treatment. Data are from experiment Btox3. Differentially expressed genes (DEGs) are shown in red.

    Journal: Journal of Experimental Botany

    Article Title: Genetic factors underlying boron toxicity tolerance in rice: genome-wide association study and transcriptomic analysis

    doi: 10.1093/jxb/erw423

    Figure Lengend Snippet: Summary of microarray analysis of two different rice varieties, MTU9 (sensitive) and SML242 (tolerant) in response to B stress treatment. Data are from experiment Btox3. Differentially expressed genes (DEGs) are shown in red.

    Article Snippet: Only samples with RNA integrity number > 8 were used for microarray slide hybridization (OakLabs GmbH, Hennigsdorf, Germany).

    Techniques: Microarray