zebrafish gene expression microarrays (v2  (Agilent technologies)

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: Identification of Estrogen Target Genes during Zebrafish Embryonic Development through Transcriptomic Analysis

doi: 10.1371/journal.pone.0079020

Figure Lengend Snippet: (A) Relative mRNA expression of the up-regulated genes vtg1 , vtg3 , vtg5 , esr1, cyp19a1b and f13a1a at different time points as determined by RT-qPCR and microarray analysis. (B) Relative mRNA expression of the down-regulated genes hpx , fkbp5 , fabp10a , agxtb , pnp4b , nlf1 , f2 , klf9 , zgc: 92590 and zgc: 110053 at different time points as determined by RT-qPCR and microarray analysis. (C) Relative mRNA expression of the non-changed genes esr2a , esr2b , rbp2a and dlgap1a at different time points as determined by RT-qPCR and microarray analysis. White bars represent microarray results and black bars RT-qPCR results. Asterisk denotes significant difference (* P <0.05, ** P <0.01; unpaired Student’s t-test compared to the controls), n≥3 biological replicates except for genes fabp10a , agxtb and zgc:110053 which were 2 biological replicates ; each replicate consists of 30 pooled embryos. Abbreviations vtg 1: vitellogenin 1 ; vtg 3: vitellogenin 3 ; vtg 5: vitellogenin 5 ; esr1 : estrogen receptor 1 ; esr2a : estrogen receptor 2a ; esr2b : estrogen receptor 2b ; cyp19a1b : cytochrome P450 , family 19, subfamily A , polypeptide 1b ; f13a1a: coagulation factor XIII, A1 polypeptide a , tandem duplicate 1; hpx : hemopexin ; fkbp5 : FK506 binding protein 5 ; fabp10a : fatty acid binding protein 10a ; agxtb : alanine-glyoxylate aminotransferase b ; pnp4b : purine nucleoside phosphorylase 4b ; nxf1 : nuclear RNA export factor 1 ; klf9 : krueppel-like factor 9 ; f2: coagulation factor II (thrombin) ; rbp2a : retinol binding protein 2a and dlgap1a : discs, large (Drosophila) homolog-associated protein 1a .

Article Snippet: Agilent zebrafish gene expression microarray v2 (part number G2519F and AMADID (design) 019161) was used for the microarray analysis.

Techniques: Expressing, Quantitative RT-PCR, Microarray, Coagulation, Binding Assay