Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.

E-GEOD-18254 - Influence of Gross Ovarian Stage on Transcript Profiles in Fathead Minnow (Pimephales promelas) Ovary Tissue

Status
Released on 30 April 2010, last updated on 27 June 2012
Organism
Pimephales promelas
Samples (30)
Array (1)
Protocols (7)
Description
Interpretation of toxicogenomic experiments conducted with ovary tissue from asynchronous-spawning small fish species are complicated by background variation in the relative abundance and proportion of follicles at different stages within the ovary tissue sample. This study employed both real-time quantitative PCR and a 15,000 gene oligonucleotide microarray to examine variation in the fathead minnow (Pimephales promelas) ovarian transcriptional profile as a function of quantitative and qualitative differences in ovarian histology. Multiple lines of evidence supported the conclusion that variation in the transcriptional profile was primarily dependent on the relative abundance of previtellogenic versus vitellogenic follicles in the ovary tissue. Due to the relatively small proportions of mature ovulated follicles or atretic follicles in the overall follicle population, few putative molecular markers of maturation, ovulation, or atresia could be identified. However, among the 460 differentially expressed genes identified in the study, targets including HtrA serine peptidase 3 (htra3), tissue inhibitor of metalloproteinase 3 (timp3), aquaporin 8 (aqp8), transgelin 2 like (tagln2), Nedd4 family interacting protein 2 (ndfip2), chemokine ligand 12a (cxcl12a), midkine related growth factor (mdka), and jagged 1b (jag 1b) exhibited responses and functional properties that support them as candidate molecular markers of significant shift in gross ovarian stage. Overall, results of this study provide insights into background variation in ovary transcript profiles that should aid and enhance the interpretation of toxicogenomic data generated in experiments conducted with small, asynchronous spawning fish species. Relative abundance of approximately 15,000 RNA transcripts in 26 ovary samples and 4 expelled oocyte (egg) samples, representing the five different histoclasses defined for the present study, was evaluated using fathead minnow oligonucleotide microarrays. Fathead minnow 15,000 gene arrays were purchased from Agilent (Palo Alto, CA, USA). The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations. One ug of total RNA was used for all hybridizations. cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer’s kits and protocols (Quick Amp Labeling kit; Agilent, Palo Alto, CA). An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc., city, state) was used to scan microarray images at 5 μm resolution.
Experiment type
transcription profiling by array 
Contacts
Natalia Vinas <natalia@icnanotox.org>, Anne L Linnum, Dalma Martinovic, Daniel L Villeneuve, Edward J Perkins, Gerald T Ankley, Jenna E Cavallin, Leah C Wehmas, Michael D Kahl, Natalia Garcia-Reyero, Nathaniel D Mueller
Citation
Influence of ovarian stage on transcript profiles in fathead minnow (Pimephales promelas) ovary tissue. Villeneuve DL, Garcia-Reyero N, Martinović D, Cavallin JE, Mueller ND, Wehmas LC, Kahl MD, Linnum AL, Perkins EJ, Ankley GT. , PMID:20363515
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-18254.idf.txt
Sample and data relationshipE-GEOD-18254.sdrf.txt
Raw data (1)E-GEOD-18254.raw.1.zip
Processed data (1)E-GEOD-18254.processed.1.zip
Array designA-GEOD-9248.adf.txt
Links