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: Nanomaterials

Article Title: A New Look at the Effects of Engineered ZnO and TiO 2 Nanoparticles: Evidence from Transcriptomics Studies

doi: 10.3390/nano12081247

Figure Lengend Snippet: Transcriptomic characterization of exposures to ZnO NPs in in vitro and in vivo studies.

Article Snippet: The combination of a well-established zebrafish model organism, and species-specific oligo microarray platform (Agilent, Santa Clara, CA, USA) and RSEQ strategies provide tools for studies on the molecular mechanisms underlying the adaptive response of fish to NPs, and they aid in the identification of NP-specific genes and signaling pathways in fish.

Techniques: In Vitro, In Vivo, Microarray, Binding Assay, Expressing, Derivative Assay, Animal Model, Cell Culture

Journal: Nanomaterials

Article Title: A New Look at the Effects of Engineered ZnO and TiO 2 Nanoparticles: Evidence from Transcriptomics Studies

doi: 10.3390/nano12081247

Figure Lengend Snippet: Transcriptomic characterization of exposures to TiO 2 NPs in in vitro and in vivo studies.

Article Snippet: The combination of a well-established zebrafish model organism, and species-specific oligo microarray platform (Agilent, Santa Clara, CA, USA) and RSEQ strategies provide tools for studies on the molecular mechanisms underlying the adaptive response of fish to NPs, and they aid in the identification of NP-specific genes and signaling pathways in fish.

Techniques: In Vitro, In Vivo, Microarray, Chemotaxis Assay, Activation Assay, Animal Model, Expressing, Transduction, Cell Differentiation, Activity Assay, Coagulation

Journal: Nanomaterials

Article Title: A New Look at the Effects of Engineered ZnO and TiO 2 Nanoparticles: Evidence from Transcriptomics Studies

doi: 10.3390/nano12081247

Figure Lengend Snippet: Transcriptomic characterization of exposures to ZnO and TiO 2 NPs in ecotoxicology-related models.

Article Snippet: The combination of a well-established zebrafish model organism, and species-specific oligo microarray platform (Agilent, Santa Clara, CA, USA) and RSEQ strategies provide tools for studies on the molecular mechanisms underlying the adaptive response of fish to NPs, and they aid in the identification of NP-specific genes and signaling pathways in fish.

Techniques: Microarray, Binding Assay, Homologous Recombination, Cell Differentiation, Transformation Assay, Modification

Journal: PLoS Genetics

Article Title: Retinoic Acid Signaling Regulates Differential Expression of the Tandemly-Duplicated Long Wavelength-Sensitive Cone Opsin Genes in Zebrafish

doi: 10.1371/journal.pgen.1005483

Figure Lengend Snippet: A. Statistical Analysis of Microarray (SAM) plot, at a 0.109 false discovery rate (FDR). B. Gene ontology (GO) analysis; selected GO categories shown. C. Venn diagram comparing differentially expressed genes in eyes of RA-treated embryos with those of RA-treated whole embryos during somitogenesis and with those of hearts of RA-treated larvae.

Article Snippet: The data were compared to those obtained using Affymetrix platform-based microarray analysis of RA treatments in zebrafish embryos, over different developmental times or in different tissues [ , ].

Techniques: Microarray

Journal: PLoS Genetics

Article Title: Retinoic Acid Signaling Regulates Differential Expression of the Tandemly-Duplicated Long Wavelength-Sensitive Cone Opsin Genes in Zebrafish

doi: 10.1371/journal.pgen.1005483

Figure Lengend Snippet: A. cyp26b1 . B. hoxb6a . C. socs3a . D. dkk1b . E. sfrp1a . F. wnt 11 . G. and J. opn1lw1 . H. and K. opn1lw2 . I. rod opsin ( RH1 ). White boxes, DMSO; gray boxes, at-RA (both in embryonic eye tissues); dark gray boxes, 9-cis RA (in whole embryos). In the boxplots, the boxes demarcate the 25 th and 75 th percentiles, dark horizontal lines designate the medians, and whiskers represent the upper and lower limits. Genes in A-C, E-G, were all identified as upregulated by the microarray; dkk1b was identified as downregulated; opn1w2 and rod opsin were not detected as differentially expressed. ***, p<0.001; **, p<0.01; *, p<0.05 (2-tailed Student’s t-test).

Article Snippet: The data were compared to those obtained using Affymetrix platform-based microarray analysis of RA treatments in zebrafish embryos, over different developmental times or in different tissues [ , ].

Techniques: Microarray