Pimephales promelas
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ABSTRACT:
PROVIDER: PRJNA167623 | ENA |
REPOSITORIES: ENA
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Project description:Fathead minnow and zebrafish are among the most intensively studied fish species in environmental toxicogenomics. To aid the assessment and interpretation of subtle transcriptomic effects from treatment conditions of interest, there needs to be a better characterization and understanding of the natural variation in gene expression among fish individuals within populations. Little effort, however, has been made in this area. Leveraging the transcriptomics data from a number of our toxicogenomics studies conducted over the years, we conducted a meta-analysis of nearly 600 microarrays generated from the ovary tissue of untreated, reproductively mature fathead minnow and zebrafish samples. As expected, there was considerable batch-to-batch transcriptomic variation; this “batch-effect” appeared to impact the fish transcriptomes randomly. The overall level of variation within-batch was quite low in fish ovary tissue, making it a suitable system for studying chemical stressors with subtle biological effects. The within-batch variation, however, differed considerably among individual genes and molecular pathways. This difference in variability is probably both technical and biological, thus suggesting a need to take into account both the expression levels and variance in evaluating and interpreting the transcriptional impact on genes and pathways by experimental conditions. There was significant conservation of both the genomes and transcriptomes between fathead minnow and zebrafish. The conservation to such a degree would enable not only a comparative biology approach in studying the mechanisms of action underlying environmental stressors, but also effective sharing of a large amount of existing public transcriptomics data for future development of toxicogenomics applications. total RNA from the ovary tissue of treated or control fish labeled in single color was hybridized to Agilent fathead minnow microarray (design 019597)
2015-08-01 | E-GEOD-60126 | biostudies-arrayexpress
Project description:The effects of progesterone on the fathead minnow testis
| PRJNA167622 | ENA
Project description:Omics approaches are broadly used to explore endocrine and toxicity-related pathways and functions. Nevertheless, there is still a significant gap in knowledge in terms of understanding the endocrine system and its numerous connections and intricate feedback loops, especially in non-model organisms. The fathead minnow (Pimephales promelas) is a widely used small fish model for aquatic toxicology and regulatory testing, particularly in North America. A draft genome has been published but the amount of available genomic or transcriptomic information is still far behind that of other more broadly studied species, such as the zebrafish. Here, we surveyed the tissue-specific proteome and transcriptome profiles in adult male fathead minnow. To do so, we generated a draft transcriptome using short and long sequencing reads. We also performed RNA sequencing and proteomics analysis on the telencephalon, hypothalamus, liver, and gut of male fish. The main purpose of this analysis was to generate tissue-specific omics data in order to support future aquatic ecotoxicogenomic and endocrine-related studies as well as to improve our understanding of the fathead minnow as an ecological model.
2018-10-15 | PXD010216 | Pride
Project description:Fathead minnow and zebrafish are among the most intensively studied fish species in environmental toxicogenomics. To aid the assessment and interpretation of subtle transcriptomic effects from treatment conditions of interest, there needs to be a better characterization and understanding of the natural variation in gene expression among fish individuals within populations. Little effort, however, has been made in this area. Leveraging the transcriptomics data from a number of our toxicogenomics studies conducted over the years, we conducted a meta-analysis of nearly 600 microarrays generated from the ovary tissue of untreated, reproductively mature fathead minnow and zebrafish samples. As expected, there was considerable batch-to-batch transcriptomic variation; this “batch-effect” appeared to impact the fish transcriptomes randomly. The overall level of variation within-batch was quite low in fish ovary tissue, making it a suitable system for studying chemical stressors with subtle biological effects. The within-batch variation, however, differed considerably among individual genes and molecular pathways. This difference in variability is probably both technical and biological, thus suggesting a need to take into account both the expression levels and variance in evaluating and interpreting the transcriptional impact on genes and pathways by experimental conditions. There was significant conservation of both the genomes and transcriptomes between fathead minnow and zebrafish. The conservation to such a degree would enable not only a comparative biology approach in studying the mechanisms of action underlying environmental stressors, but also effective sharing of a large amount of existing public transcriptomics data for future development of toxicogenomics applications.
2015-08-01 | GSE60126 | GEO
Project description:Influence of Gross Ovarian Stage on Transcript Profiles in Fathead Minnow (Pimephales promelas) Ovary Tissue
| PRJNA119595 | ENA
Project description:Transcriptional signature of progesterone-induced germinal vesicle breakdown in the fathead minnow ovary (Pimephales promelas)
| PRJNA186798 | ENA
Project description:The herbicide linuron is an endocrine disruptor with a suspected anti-androgenic mode of action (MOA) but the complete MOA for LIN is not fully characterized. The objectives of this study were to better characterize the MOA of LIN in the fathead minnow (FHMs) ovary by comparing expression profiles of LIN to dihydrotestosterone (DHT) and flutamide (FLUT), both model compounds with well defined androgenic and anti-androgenic MOAs respectively. Ovarian explants from vitellogenic FHMs were exposed to 10-6 M, 10-7 M, and 10-8 M of DHT, FLUT, and LIN in vitro in a12 hour incubation experiment. Ovary explants exposed to DHT showed a significant increase in E2 production compared to controls but FLUT and LIN did not affect E2 production. Microarray analysis and support vector machine classification revealed that expression patterns of FLUT and LIN in the ovary were more similar to each other compared to DHT and other androgens. Gene set enrichment analysis identified the notch signaling cascade was affected by all three chemicals. DHT down-regulated the WNT-Frizzled pathway while LIN down-regulated angiopoietin receptor signaling and increased biosynthesis of cholesterol. LIN shared 27 expression sub-networks (e.g. beta-3 adrenergic receptor, MAP3K1, interleukin, signlaing) in common with FLUT, and only 4 sub-networks with DHT. A reciprocal gene expression network was constructed using DHT and FLUT data, and the network revealed that steroid metabolism, translation, and DNA replication are potentially regulated through AR signaling. This study characterizes cell pathways associated with E2 production and identifies cell signaling cascades that may be disrupted by ureic-based herbicides in the ovary. 16 samples total; 4 control, 4 DHT, 4 Flutamide, 4 LIN
2012-07-01 | E-GEOD-38287 | biostudies-arrayexpress
Project description:Effects of trenbolone, flutamide and a mix of both in fathead minnow ovaries
| PRJNA111185 | ENA
Project description:The herbicide linuron is an endocrine disruptor with a suspected anti-androgenic mode of action (MOA) but the complete MOA for LIN is not fully characterized. The objectives of this study were to better characterize the MOA of LIN in the fathead minnow (FHMs) ovary by comparing expression profiles of LIN to dihydrotestosterone (DHT) and flutamide (FLUT), both model compounds with well defined androgenic and anti-androgenic MOAs respectively. Ovarian explants from vitellogenic FHMs were exposed to 10-6 M, 10-7 M, and 10-8 M of DHT, FLUT, and LIN in vitro in a12 hour incubation experiment. Ovary explants exposed to DHT showed a significant increase in E2 production compared to controls but FLUT and LIN did not affect E2 production. Microarray analysis and support vector machine classification revealed that expression patterns of FLUT and LIN in the ovary were more similar to each other compared to DHT and other androgens. Gene set enrichment analysis identified the notch signaling cascade was affected by all three chemicals. DHT down-regulated the WNT-Frizzled pathway while LIN down-regulated angiopoietin receptor signaling and increased biosynthesis of cholesterol. LIN shared 27 expression sub-networks (e.g. beta-3 adrenergic receptor, MAP3K1, interleukin, signlaing) in common with FLUT, and only 4 sub-networks with DHT. A reciprocal gene expression network was constructed using DHT and FLUT data, and the network revealed that steroid metabolism, translation, and DNA replication are potentially regulated through AR signaling. This study characterizes cell pathways associated with E2 production and identifies cell signaling cascades that may be disrupted by ureic-based herbicides in the ovary.
2012-07-02 | GSE38287 | GEO