The transcriptomic response to finasteride in the Silurana tropicalis testis
Ontology highlight
ABSTRACT:
ORGANISM(S): Xenopus tropicalis
PROVIDER: GSE46366 | GEO | 2014/04/01
SECONDARY ACCESSION(S): PRJNA198905
REPOSITORIES: GEO
Similar Datasets
Project description:An ex vivo protocol was optimized to expose testis tissues from juvenile Silurana tropicalis to 5 uM finasteride. Testis tissues were incubated in L-15 media with (n = 8) and without (n = 8) finasteride for 6 h at 26 °C on top of an orbital shaker. Afterwards, the tissues were flash frozen on dry ice and RNA was isolated using Trizol. The isolated RNA of four control tissue samples and four finasteride exposed tissue samples were then analyzed using a custom microarray for S. tropicalis containing 44,000 probes . Testis tissues were incubated in L-15 media with (n = 8) and without (n = 8) finasteride for 6 h at 26 °C
2014-04-01 | E-GEOD-46366 | biostudies-arrayexpress
Project description:The transcriptomic response to finasteride in the Silurana tropicalis testis
| PRJNA198905 | ENA
Project description:Arsenic is a carcinogenic metalloid element found naturally in the environment; however human activities such as mining and pesticide use have led to increased concentrations in some areas. Silurana tropicalis eggs were exposed to sublethal concentrations of sodium arsenate (0, 0.5 and 1 ppm) for 3 days during embryogenesis. Four pooled of 10 larvae were sampled per treatment and analyzed for gene expression changes using a microarray approach. Silurana tropicalis eggs were exposed to sublethal concentrations of sodium arsenate (0, 0.5 and 1 ppm) for 3 days during embryogenesis. There were 5 controls, 5 low dose and 6 high dose microarrays perfomed.
2014-07-31 | E-GEOD-57673 | biostudies-arrayexpress
Project description:Arsenic is a carcinogenic metalloid element found naturally in the environment; however human activities such as mining and pesticide use have led to increased concentrations in some areas. Silurana tropicalis eggs were exposed to sublethal concentrations of sodium arsenate (0, 0.5 and 1 ppm) for 3 days during embryogenesis. Four pooled of 10 larvae were sampled per treatment and analyzed for gene expression changes using a microarray approach.
2014-07-31 | GSE57673 | GEO
Project description:Naphthenic acids (Nas) are carboxylic acids present in crude oil and classfied as emergent pollutants. The mechanisms underlaying the toxicity of such mixtures are unknown. Changes in gene expression are expected to reflect te teratogenenic effects of the exposure to NAs. The objective of these experiments is to determine the changes in the gene expression profile of Silurana (Xenopus) tropicalis embryos due to the exposition to two NA mixtures.
2018-11-29 | GSE118736 | GEO
Project description:Dyes used in fabric and leather industry are being released and accumulated into Canadian ecosystems. Recent studies have demonstrated that dyes made of azo compounds significantly increase toxicity in biota, which is explained by their toxic metabolites (e.g., aromatic amines). The metabolites of azo compounds interact with hydrophobic surfaces of cell membranes causing expansion of the membrane which impede normal cellular functions. It has been suggested that this process leads to cell death due to improper ion balance. Currently, it is estimated that between 10 and 15% of azo dyes are released in the environment as effluent. The aim of this study was to evaluate toxicity and gene networks altered by azo compounds in amphibians using ecotoxicogenomic approaches. Larvae of the frog Silurana tropicalis (Western clawed frog) were exposed to sediment contaminated to 887 ppm Disperse Yellow 7 (DY7). Larvae were exposed from Nieuwkoop-Faber developmental stage 12 to 46. Data suggest that the azo dye DY7 induced cellular stress and interfered with androgen biosynthesis in early tadpole development. At exposure completion, RNA was isolated from whole larvae and quality was ascertained using bioanalyzer analysis. A custom Agilent 4 X 44 K microarray for S. tropicalis was used to characterize gene regulatory networks underlying toxicity. This study presents the transcriptional regulatory pathways affected by DY7 in S. tropicalis early development.
2012-11-30 | GSE40149 | GEO
Project description:Dyes used in fabric and leather industry are being released and accumulated into Canadian ecosystems. Recent studies have demonstrated that dyes made of azo compounds significantly increase toxicity in biota, which is explained by their toxic metabolites (e.g., aromatic amines). The metabolites of azo compounds interact with hydrophobic surfaces of cell membranes causing expansion of the membrane which impede normal cellular functions. It has been suggested that this process leads to cell death due to improper ion balance. Currently, it is estimated that between 10 and 15% of azo dyes are released in the environment as effluent. The aim of this study was to evaluate toxicity and gene networks altered by azo compounds in amphibians using ecotoxicogenomic approaches. Larvae of the frog Silurana tropicalis (Western clawed frog) were exposed to sediment contaminated to 887 ppm Disperse Yellow 7 (DY7). Larvae were exposed from Nieuwkoop-Faber developmental stage 12 to 46. Data suggest that the azo dye DY7 induced cellular stress and interfered with androgen biosynthesis in early tadpole development. At exposure completion, RNA was isolated from whole larvae and quality was ascertained using bioanalyzer analysis. A custom Agilent 4 X 44 K microarray for S. tropicalis was used to characterize gene regulatory networks underlying toxicity. This study presents the transcriptional regulatory pathways affected by DY7 in S. tropicalis early development. Embryos were exposed to the DY7 dye during development. There were 4 control groups exposed and 4 treatment groups exposed.
2012-11-30 | E-GEOD-40149 | biostudies-arrayexpress
Project description:African clawed frog Xenopus sp. is used extensively for developmental biology and toxicology research. Amid concerns of environmental pollutants disrupting endocrine systems and causing altered reproductive development in wildlife, eco-toxicology research has led to a focus on linking molecular initiating events to population-level effects. As such, efforts to better understand reproductive development at the molecular level in these model species are warranted. To that end, transcriptomes were characterized in differentiating Xenopus tropicalis gonad tissues at Nieuwkoop and Faber (NF) stage 58 (pro-metamorphosis), NF66 (completion of metamorphosis), one week post-metamorphosis (1WPM), and two weeks post-metamorphosis (2WPM). Differential expression analysis between tissue types at each developmental stage revealed a substantial divergence of ovary and testis transcriptomes starting between NF58 and NF66; transcriptomes continued to diverge through 2WPM. Generally, testis-enriched transcripts were expressed at relatively constant levels, while ovary-enriched transcripts were up-regulated within this developmental period. Functional analyses of differentially expressed transcripts allowed linkages to be made between their putative human orthologues and specific cellular processes associated with differentiating gonad tissues. In ovary tissue, genetic programs direct germ cells through meiosis to the diplotene stage when maternal mRNAs are transcribed and trafficked to oocytes for translation following fertilization. In the testis, gene expression is consistent with connective tissue development, tubule formation, and germ cell support (Leydig and Sertoli cells). This dataset exhibited remarkable consistency with transcript profiles previously described in gonad tissues across species, and emphasizes the universal importance of certain transcripts for germ cell development and preparation of these tissues for reproduction.
2014-07-31 | GSE58612 | GEO
Project description:Gene set and sub-network enrichment analysis provides an integrated approach for identifying gene regulatory networks underlying development. Anuran development is a coordinated process, and levels of mRNA are first dominated by maternally deposited genes, followed by active transcription of embryonic genes as the embryo undergoes morphogenesis and organ formation. The objectives of this study were to characterize early gene regulatory networks underlying Silurana tropicalis development. A custom Agilent 4 x 44 K microarray was developed to characterize networks during early development (1, 17, 36, 96 hpf). Cluster analysis revealed that each stage showed unique gene expression profiles and that 1 hpf was most different than the other three stages. There were > 8000 unique gene probes (p<0.01, FDR = 5%) that were differentially expressed between 1 hpf (2 cell stage) and 17 hpf and > 2000 gene probes differentially expressed between 36 hpf and 96 hpf. Genes higher in abundance (>100-fold) at 1 hpf compared to 17 hpf included oocyte-specific histone RNA stem-loop-binding protein 2, mitogen-activated protein kinase 14, and cyclin B5, suggesting these transcripts are maternally inherited or actively transcribed at fertilization. Gene ontology revealed that genes involved in nucleosome assembly, cell division, pattern specification, neurotransmission, and general metabolism were increasingly regulated throughout development, consistent with active development. In the period between 17-36 hpf, gene networks that play a role in organogenesis and organ function, including those related to the heart (heart morphogenesis, central nervous system (olfactory bulb development, dopamine metabolism), and kidney (renal reabsorption, water balance) were activated while between 36-96 hpf, networks involving in gut development, immune responses, lipid metabolism, hormone signaling, and brain development were prevalent. This study increases understanding of the spatiotemporal S. tropicalis embryonic development using gene regulatory networks.
2012-07-31 | GSE38576 | GEO
Project description:Gene set and sub-network enrichment analysis provides an integrated approach for identifying gene regulatory networks underlying development. Anuran development is a coordinated process, and levels of mRNA are first dominated by maternally deposited genes, followed by active transcription of embryonic genes as the embryo undergoes morphogenesis and organ formation. The objectives of this study were to characterize early gene regulatory networks underlying Silurana tropicalis development. A custom Agilent 4 x 44 K microarray was developed to characterize networks during early development (1, 17, 36, 96 hpf). Cluster analysis revealed that each stage showed unique gene expression profiles and that 1 hpf was most different than the other three stages. There were > 8000 unique gene probes (p<0.01, FDR = 5%) that were differentially expressed between 1 hpf (2 cell stage) and 17 hpf and > 2000 gene probes differentially expressed between 36 hpf and 96 hpf. Genes higher in abundance (>100-fold) at 1 hpf compared to 17 hpf included oocyte-specific histone RNA stem-loop-binding protein 2, mitogen-activated protein kinase 14, and cyclin B5, suggesting these transcripts are maternally inherited or actively transcribed at fertilization. Gene ontology revealed that genes involved in nucleosome assembly, cell division, pattern specification, neurotransmission, and general metabolism were increasingly regulated throughout development, consistent with active development. In the period between 17-36 hpf, gene networks that play a role in organogenesis and organ function, including those related to the heart (heart morphogenesis, central nervous system (olfactory bulb development, dopamine metabolism), and kidney (renal reabsorption, water balance) were activated while between 36-96 hpf, networks involving in gut development, immune responses, lipid metabolism, hormone signaling, and brain development were prevalent. This study increases understanding of the spatiotemporal S. tropicalis embryonic development using gene regulatory networks. Gene expression analysis was performed with four biological replicates for four developmental stages (n = 16). Stages were NF stages 2, 16, 34, and 46.
2012-07-30 | E-GEOD-38576 | biostudies-arrayexpress