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Series GSE18254 Query DataSets for GSE18254
Status Public on May 01, 2010
Title Influence of Gross Ovarian Stage on Transcript Profiles in Fathead Minnow (Pimephales promelas) Ovary Tissue
Organism Pimephales promelas
Experiment type Expression profiling by array
Summary 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.
 
Overall design 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.
 
Contributor(s) Villeneuve DL, Garcia-Reyero N, Martinovic D, Cavallin JE, Mueller ND, Wehmas LC, Kahl MD, Linnum AL, Perkins EJ, Ankley GT
Citation(s) 20363515
Submission date Sep 24, 2009
Last update date Jul 22, 2013
Contact name Natalia Vinas
E-mail(s) natalia@icnanotox.org, nataliarv@gmail.com
Phone 6016343764
Organization name Mississippi State University
Street address 3909 Halls Ferry Rd
City Vicksburg
State/province MS
ZIP/Postal code 39180
Country USA
 
Platforms (1)
GPL9248 Agilent-019597 FHM_Denslow_8x15K [Feature Number version]
Samples (30)
GSM456136 Atretic - 1
GSM456137 Atretic - 2
GSM456138 Atretic - 3
Relations
BioProject PRJNA119595

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE18254_RAW.tar 68.3 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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