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zebrafish microarray platform  (Agilent technologies)


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    Structured Review

    Agilent technologies zebrafish microarray platform
    Of 12261 potential unique genes, the mRNA expression of 1313 were found to be statistically significantly changed at 24 hpf, with 583 downregulated (grey) and 730 upregulated (black). 836 genes were changed with statistical significance at 36 hpf, of which 243 were downregulated and 593 were upregulated. (n=3 pools of 25 embryos used for <t>microarray</t> analysis, P≤0.05, Students t -test with Benjamini-Hochberg false-discovery rate correction).
    Zebrafish Microarray Platform, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/zebrafish+microarray/pmc03858477-91-29-28
    Average 90 stars, based on 1 article reviews
    zebrafish microarray platform - by Bioz Stars, 2026-09
    90/100 stars

    Images

    1) Product Images from "The Transcriptomics of Glucocorticoid Receptor Signaling in Developing Zebrafish"

    Article Title: The Transcriptomics of Glucocorticoid Receptor Signaling in Developing Zebrafish

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0080726

    Of 12261 potential unique genes, the mRNA expression of 1313 were found to be statistically significantly changed at 24 hpf, with 583 downregulated (grey) and 730 upregulated (black). 836 genes were changed with statistical significance at 36 hpf, of which 243 were downregulated and 593 were upregulated. (n=3 pools of 25 embryos used for microarray analysis, P≤0.05, Students t -test with Benjamini-Hochberg false-discovery rate correction).
    Figure Legend Snippet: Of 12261 potential unique genes, the mRNA expression of 1313 were found to be statistically significantly changed at 24 hpf, with 583 downregulated (grey) and 730 upregulated (black). 836 genes were changed with statistical significance at 36 hpf, of which 243 were downregulated and 593 were upregulated. (n=3 pools of 25 embryos used for microarray analysis, P≤0.05, Students t -test with Benjamini-Hochberg false-discovery rate correction).

    Techniques Used: Expressing, Microarray

    qPCR analysis was performed on 7 genes to confirm the transcript abundance seen with the microarray analysis. The selected genes were bmp7a (A), f5 (B) , ff1d (C), myom1a (D), pomca (E), star (F), mc1r (G). Data is presented as mean ± standard error of the mean (normalized to β-actin, SEM; n=5-7 pools of 25 embryos each); * denotes statistical significance ( t -test, p<0.05). (See for fold-changes and p-values).
    Figure Legend Snippet: qPCR analysis was performed on 7 genes to confirm the transcript abundance seen with the microarray analysis. The selected genes were bmp7a (A), f5 (B) , ff1d (C), myom1a (D), pomca (E), star (F), mc1r (G). Data is presented as mean ± standard error of the mean (normalized to β-actin, SEM; n=5-7 pools of 25 embryos each); * denotes statistical significance ( t -test, p<0.05). (See for fold-changes and p-values).

    Techniques Used: Microarray

    List of genes confirmed using  microarray  and qPCR with fold-changes and p-values.
    Figure Legend Snippet: List of genes confirmed using microarray and qPCR with fold-changes and p-values.

    Techniques Used: Microarray

    Related Articles

    Microarray:

    Article Title: Nrf2 and Nrf2-Related Proteins in Development and Developmental Toxicity: Insights from studies in Zebrafish (Danio rerio)
    Article Snippet: .. Here, the 20 mammalian candidate genes have been collapsed into 15 sets based on orthologous or co-orthologous relationships with zebrafish genes and including only those genes with orthologs represented on the Agilent zebrafish microarray. ..

    Article Title: RNA isolation method for single embryo transcriptome analysis in zebrafish
    Article Snippet: .. To further assess the quality of the isolated RNA, the mRNA from each sample was amplified, labeled, and hybridized on a custom Agilent 8 × 15 k zebrafish microarray using standard microarray procedures. ..

    Article Title: The Transcriptomics of Glucocorticoid Receptor Signaling in Developing Zebrafish
    Article Snippet: .. To better understand of the molecular mechanisms involved, we investigated changes in the developmental transcriptome prior to hatch, in response to morpholino oligonucleotide knockdown of GR using the Agilent zebrafish microarray platform. ..

    Article Title: The Transcriptional Response to Oxidative Stress during Vertebrate Development: Effects of tert -Butylhydroquinone and 2,3,7,8-Tetrachlorodibenzo- p -Dioxin
    Article Snippet: .. Importantly, there was concordance between microarray and qRT-PCR data , validating the Agilent zebrafish microarray as a platform for evaluating expression profiles and for gene discovery in developing zebrafish exposed to oxidants. ..

    Article Title: Inhibition of endogenous MTF-1 signaling in zebrafish embryos identifies novel roles for MTF-1 in development
    Article Snippet: .. The authors would like to thank Drs. Jared V. Goldstone and John J. Stegeman from Woods Hole Oceanographic Institution for access to the custom zebrafish microarray design thru Agilent Technologies (Santa Clara, CA, USA). ..

    Article Title: Foxq2 determines blue cone identity in zebrafish
    Article Snippet: Quality and quantity of the resulting RNA were assessed using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies). .. Microarray analysis was performed using the Agilent 4 × 44 k Zebrafish microarray according to the manufacturer’s protocol for the two-color method. .. Cy3- or Cy5-labeled complementary RNA (cRNA) probe was synthesized from 150 ng of total RNA using the Quick-Amp Labeling Kit (Agilent Technologies).

    Article Title: Zebrafish Pou5f1-dependent transcriptional networks in temporal control of early development
    Article Snippet: .. Mouse orthologs have been identified for 8341 genes in the zebrafish Agilent microarray (conserved genes). ..

    Article Title: Foxq2 determines blue cone identity in zebrafish
    Article Snippet: Quality and quantity of the resulting RNA were assessed using a NanoDrop ND-2000 spectrophotometer (Thermo Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies). .. Microarray Analysis was performed using the Agilent 4 ×44 k Zebrafish microarray according to the manufacturer’s protocol for the two-color method. .. Cy3- or Cy5- labeled cRNA probe was synthesized from 150 ng of total RNA using the Quick-Amp Labeling Kit (Agilent Technologies).

    Isolation:

    Article Title: RNA isolation method for single embryo transcriptome analysis in zebrafish
    Article Snippet: .. To further assess the quality of the isolated RNA, the mRNA from each sample was amplified, labeled, and hybridized on a custom Agilent 8 × 15 k zebrafish microarray using standard microarray procedures. ..

    Amplification:

    Article Title: RNA isolation method for single embryo transcriptome analysis in zebrafish
    Article Snippet: .. To further assess the quality of the isolated RNA, the mRNA from each sample was amplified, labeled, and hybridized on a custom Agilent 8 × 15 k zebrafish microarray using standard microarray procedures. ..

    Labeling:

    Article Title: RNA isolation method for single embryo transcriptome analysis in zebrafish
    Article Snippet: .. To further assess the quality of the isolated RNA, the mRNA from each sample was amplified, labeled, and hybridized on a custom Agilent 8 × 15 k zebrafish microarray using standard microarray procedures. ..

    Knockdown:

    Article Title: The Transcriptomics of Glucocorticoid Receptor Signaling in Developing Zebrafish
    Article Snippet: .. To better understand of the molecular mechanisms involved, we investigated changes in the developmental transcriptome prior to hatch, in response to morpholino oligonucleotide knockdown of GR using the Agilent zebrafish microarray platform. ..

    Quantitative RT-PCR:

    Article Title: The Transcriptional Response to Oxidative Stress during Vertebrate Development: Effects of tert -Butylhydroquinone and 2,3,7,8-Tetrachlorodibenzo- p -Dioxin
    Article Snippet: .. Importantly, there was concordance between microarray and qRT-PCR data , validating the Agilent zebrafish microarray as a platform for evaluating expression profiles and for gene discovery in developing zebrafish exposed to oxidants. ..

    Expressing:

    Article Title: The Transcriptional Response to Oxidative Stress during Vertebrate Development: Effects of tert -Butylhydroquinone and 2,3,7,8-Tetrachlorodibenzo- p -Dioxin
    Article Snippet: .. Importantly, there was concordance between microarray and qRT-PCR data , validating the Agilent zebrafish microarray as a platform for evaluating expression profiles and for gene discovery in developing zebrafish exposed to oxidants. ..



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    Correlation plots indicating the relationship between qPCR results (fold change; Y- axis)) of six selected genes and the corresponding data from <t>microarray</t> analysis (X- axis). Fold changes of genes immediately after packing (0 h), and at 48 and 72 h during transport compared to the values prior to transport (basal) are displayed in the figure. Note that the fold changes for scd are 1/10 th of the actual changes.
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    Image Search Results


    Journal: Data in Brief

    Article Title: Microarray transcriptome datasets of maternal-zygotic DNA methyltransferase 3aa −/− zebrafish during early developmental stages

    doi: 10.1016/j.dib.2023.108967

    Figure Lengend Snippet:

    Article Snippet: Upon completion of the fragmentation reaction, 25 μl of 2 × Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Danio rerio (Zebrafish) Oligo Microarray V3 (Design ID: Agilent-026,437) (Agilent) for 17 h at 65 °C in a rotating Agilent hybridization oven.

    Techniques: DNA Methylation Assay, Labeling, Microarray, Hybridization, Expressing

    Of 12261 potential unique genes, the mRNA expression of 1313 were found to be statistically significantly changed at 24 hpf, with 583 downregulated (grey) and 730 upregulated (black). 836 genes were changed with statistical significance at 36 hpf, of which 243 were downregulated and 593 were upregulated. (n=3 pools of 25 embryos used for microarray analysis, P≤0.05, Students t -test with Benjamini-Hochberg false-discovery rate correction).

    Journal: PLoS ONE

    Article Title: The Transcriptomics of Glucocorticoid Receptor Signaling in Developing Zebrafish

    doi: 10.1371/journal.pone.0080726

    Figure Lengend Snippet: Of 12261 potential unique genes, the mRNA expression of 1313 were found to be statistically significantly changed at 24 hpf, with 583 downregulated (grey) and 730 upregulated (black). 836 genes were changed with statistical significance at 36 hpf, of which 243 were downregulated and 593 were upregulated. (n=3 pools of 25 embryos used for microarray analysis, P≤0.05, Students t -test with Benjamini-Hochberg false-discovery rate correction).

    Article Snippet: To better understand of the molecular mechanisms involved, we investigated changes in the developmental transcriptome prior to hatch, in response to morpholino oligonucleotide knockdown of GR using the Agilent zebrafish microarray platform.

    Techniques: Expressing, Microarray

    qPCR analysis was performed on 7 genes to confirm the transcript abundance seen with the microarray analysis. The selected genes were bmp7a (A), f5 (B) , ff1d (C), myom1a (D), pomca (E), star (F), mc1r (G). Data is presented as mean ± standard error of the mean (normalized to β-actin, SEM; n=5-7 pools of 25 embryos each); * denotes statistical significance ( t -test, p<0.05). (See for fold-changes and p-values).

    Journal: PLoS ONE

    Article Title: The Transcriptomics of Glucocorticoid Receptor Signaling in Developing Zebrafish

    doi: 10.1371/journal.pone.0080726

    Figure Lengend Snippet: qPCR analysis was performed on 7 genes to confirm the transcript abundance seen with the microarray analysis. The selected genes were bmp7a (A), f5 (B) , ff1d (C), myom1a (D), pomca (E), star (F), mc1r (G). Data is presented as mean ± standard error of the mean (normalized to β-actin, SEM; n=5-7 pools of 25 embryos each); * denotes statistical significance ( t -test, p<0.05). (See for fold-changes and p-values).

    Article Snippet: To better understand of the molecular mechanisms involved, we investigated changes in the developmental transcriptome prior to hatch, in response to morpholino oligonucleotide knockdown of GR using the Agilent zebrafish microarray platform.

    Techniques: Microarray

    List of genes confirmed using  microarray  and qPCR with fold-changes and p-values.

    Journal: PLoS ONE

    Article Title: The Transcriptomics of Glucocorticoid Receptor Signaling in Developing Zebrafish

    doi: 10.1371/journal.pone.0080726

    Figure Lengend Snippet: List of genes confirmed using microarray and qPCR with fold-changes and p-values.

    Article Snippet: To better understand of the molecular mechanisms involved, we investigated changes in the developmental transcriptome prior to hatch, in response to morpholino oligonucleotide knockdown of GR using the Agilent zebrafish microarray platform.

    Techniques: Microarray

    Of 12261 potential unique genes, the mRNA expression of 1313 were found to be statistically significantly changed at 24 hpf, with 583 downregulated (grey) and 730 upregulated (black). 836 genes were changed with statistical significance at 36 hpf, of which 243 were downregulated and 593 were upregulated. (n=3 pools of 25 embryos used for microarray analysis, P≤0.05, Students t -test with Benjamini-Hochberg false-discovery rate correction).

    Journal: PLoS ONE

    Article Title: The Transcriptomics of Glucocorticoid Receptor Signaling in Developing Zebrafish

    doi: 10.1371/journal.pone.0080726

    Figure Lengend Snippet: Of 12261 potential unique genes, the mRNA expression of 1313 were found to be statistically significantly changed at 24 hpf, with 583 downregulated (grey) and 730 upregulated (black). 836 genes were changed with statistical significance at 36 hpf, of which 243 were downregulated and 593 were upregulated. (n=3 pools of 25 embryos used for microarray analysis, P≤0.05, Students t -test with Benjamini-Hochberg false-discovery rate correction).

    Article Snippet: Global gene expression in MP and MO samples was analyzed by hybridization to the Zebrafish V2 Gene Expression Microarray (Product ID 019161; Agilent, Santa Clara, CA), after one-colour labeling with the Low Input Quick Amp Labeling Kit (Agilent).

    Techniques: Expressing, Microarray

    qPCR analysis was performed on 7 genes to confirm the transcript abundance seen with the microarray analysis. The selected genes were bmp7a (A), f5 (B) , ff1d (C), myom1a (D), pomca (E), star (F), mc1r (G). Data is presented as mean ± standard error of the mean (normalized to β-actin, SEM; n=5-7 pools of 25 embryos each); * denotes statistical significance ( t -test, p<0.05). (See for fold-changes and p-values).

    Journal: PLoS ONE

    Article Title: The Transcriptomics of Glucocorticoid Receptor Signaling in Developing Zebrafish

    doi: 10.1371/journal.pone.0080726

    Figure Lengend Snippet: qPCR analysis was performed on 7 genes to confirm the transcript abundance seen with the microarray analysis. The selected genes were bmp7a (A), f5 (B) , ff1d (C), myom1a (D), pomca (E), star (F), mc1r (G). Data is presented as mean ± standard error of the mean (normalized to β-actin, SEM; n=5-7 pools of 25 embryos each); * denotes statistical significance ( t -test, p<0.05). (See for fold-changes and p-values).

    Article Snippet: Global gene expression in MP and MO samples was analyzed by hybridization to the Zebrafish V2 Gene Expression Microarray (Product ID 019161; Agilent, Santa Clara, CA), after one-colour labeling with the Low Input Quick Amp Labeling Kit (Agilent).

    Techniques: Microarray

    List of genes confirmed using  microarray  and qPCR with fold-changes and p-values.

    Journal: PLoS ONE

    Article Title: The Transcriptomics of Glucocorticoid Receptor Signaling in Developing Zebrafish

    doi: 10.1371/journal.pone.0080726

    Figure Lengend Snippet: List of genes confirmed using microarray and qPCR with fold-changes and p-values.

    Article Snippet: Global gene expression in MP and MO samples was analyzed by hybridization to the Zebrafish V2 Gene Expression Microarray (Product ID 019161; Agilent, Santa Clara, CA), after one-colour labeling with the Low Input Quick Amp Labeling Kit (Agilent).

    Techniques: Microarray

    Correlation plots indicating the relationship between qPCR results (fold change; Y- axis)) of six selected genes and the corresponding data from microarray analysis (X- axis). Fold changes of genes immediately after packing (0 h), and at 48 and 72 h during transport compared to the values prior to transport (basal) are displayed in the figure. Note that the fold changes for scd are 1/10 th of the actual changes.

    Journal: PLoS ONE

    Article Title: Liver Transcriptome Changes in Zebrafish during Acclimation to Transport-Associated Stress

    doi: 10.1371/journal.pone.0065028

    Figure Lengend Snippet: Correlation plots indicating the relationship between qPCR results (fold change; Y- axis)) of six selected genes and the corresponding data from microarray analysis (X- axis). Fold changes of genes immediately after packing (0 h), and at 48 and 72 h during transport compared to the values prior to transport (basal) are displayed in the figure. Note that the fold changes for scd are 1/10 th of the actual changes.

    Article Snippet: Significantly regulated probes at 0, 48 and 72 h, compared to basal levels, were subjected to GO enrichment analysis using the GOEAST web based software ( http://omicslab.genetics.ac.cn/GOEAST/index.php ) with the Agilent Zebrafish V3 gene expression microarray as reference.

    Techniques: Microarray