nimblegen zebrafish microarrays  (MOgene Inc)

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

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

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

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

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

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

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

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