Journal: BMC Medical Genomics

Article Title: Molecular conservation of estrogen-response associated with cell cycle regulation, hormonal carcinogenesis and cancer in zebrafish and human cancer cell lines

doi: 10.1186/1755-8794-4-41

Figure Lengend Snippet: Validation of microarray data by qRT-PCR . A . Expression levels of vtg1 and vtg3 and B . esr1 . C . Selection of representative up-regulated genes. D . Selection of representative down-regulated genes. The data represents average of 3 replicates and presented as mean and standard deviation.

Article Snippet: Compugen microarray set (Compugen, USA) containing 16,416 oligonucleotide probes representing zebrafish genes was used in this study.

Techniques: Microarray, Quantitative RT-PCR, Expressing, Selection, Standard Deviation

Journal: BMC Genomics

Article Title: From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis

doi: 10.1186/1471-2164-8-358

Figure Lengend Snippet: Hierarchical clustering of genes showing significant gene regulation in response to environmental stress . The results of hierarchical clustering of genes that showed differential expression in response to different types of environmental stress in Pomacentrus moluccensis are shown in form of a heat map. Values presented are the values of the t-statistic summarising the expression responses across biological replicates. Where spots on the microarray could be unambiguously annotated with gene names, these are given to the right of the corresponding row in the heat map. Three genes that showed the most consistent induction across stress treatments are in bold. "3 h" indicates three hour exposure, "5 d" five day exposure to stressor.

Article Snippet: While there are currently no species-specific microarrays available for any species of coral reef fish, we have previously shown that the Compugen 16 K oligonucleotide microarray developed for the zebrafish, Danio rerio , can be successfully used to study gene responses in the coral reef fish Pomacentrus moluccensis [ ].

Techniques: Quantitative Proteomics, Expressing, Microarray

Journal: BMC Genomics

Article Title: From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis

doi: 10.1186/1471-2164-8-358

Figure Lengend Snippet: Experimental design of the multi-stressor approach to investigate environmental stress responses . The experiments were performed in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis . Text within each circle names the stress and the duration it was applied, being three hours (3 h) or five days (5 d). Numbers above arrows indicate the number of microarray hybridisations used in the analysis of gene expression changes. Each microarray hybridisation compared relative expression levels in two samples (two-colour microarray analysis). Each sample in the microarray hybridisations represented one individual fish (no sample pooling) and a total of 118 individual fish were analysed in this study. Arrowheads indicate use of Alexa Fluor ® 555 dye (green), which was swapped between samples to account for potential dye bias. The dotted lines within the ambient 3 h group indicate five groups of fish exposed to ambient conditions on separate days in order to provide time-matched controls for each of the stress treatments. Ambient conditions were 28°C in summer and 26°C in winter.

Article Snippet: While there are currently no species-specific microarrays available for any species of coral reef fish, we have previously shown that the Compugen 16 K oligonucleotide microarray developed for the zebrafish, Danio rerio , can be successfully used to study gene responses in the coral reef fish Pomacentrus moluccensis [ ].

Techniques: Microarray, Gene Expression, Hybridization, Expressing