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Series GSE93635 Query DataSets for GSE93635
Status Public on Feb 20, 2017
Title Atrazine Exposure Elicits Copy Number Alterations in the Zebrafish Genome
Organism Danio rerio
Experiment type Genome variation profiling by genome tiling array
Summary Atrazine is an agricultural herbicide used throughout the Midwestern United States that frequently contaminates potable water supplies resulting in human exposure. Using the zebrafish model system, an embryonic atrazine exposure was previously reported to decrease spawning rates with an increase in progesterone and ovarian follicular atresia in adult females. In addition, alterations in genes associated with distinct molecular pathways of the endocrine system were observed in brain and gonad tissue of the adult females and males. Current hypotheses for mechanistic changes in the developmental origins of health and disease include genetic (e.g., copy number alterations) or epigenetic (e.g., DNA methylation) mechanisms. As such, in the current study we investigated whether an atrazine exposure would generate copy number alterations (CNAs) in the zebrafish genome. A zebrafish fibroblast cell line was used to limit detection to CNAs caused by the chemical exposure. First, cells were exposed to a range of atrazine concentrations and a crystal violet assay was completed, showing confluency decreased by ~60% at 46.3 µM. Cells were then exposed to 0, 0.463, 4.63, or 46.3 µM atrazine and array comparative genomic hybridization completed. Results showed 34, 21, and 44 CNAs in the 0.463, 4.63, and 46.3µM treatments, respectively. Furthermore, CNAs were associated with previously reported gene expression alterations in adult male and female zebrafish. This study demonstrates that atrazine exposure can generate CNAs that are linked to gene expression alterations observed in adult zebrafish exposed to atrazine during embryogenesis providing a mechanism of the developmental origins of atrazine endocrine disruption.
 
Overall design The objective of this study was to identify whether an atrazine exposure will generate copy number alterations. First, a zebrafish fibroblast cell line was exposed to a range of atrazine concentrations (0-1.125 mM) to determine concentrations where cell confluency would be altered (n=4 plates with 4 subsamples of each treatment concentration on each plate). From this experiment, treatment concentrations (0, 0.463, 4.63 and 46.3 um atrazine) were chosen to represent a range from no effect on confluency to decreasing cell confuency to ~60% in this cell line. Cells were then exposed to these four treatment concentrations and array CGH was used to detect copy number aberrations (CNAs) in atrazine treatments compared to the control treatment (n=3). qPCR was used to confirm CNAs. CNAs were compared to gene expression microarray data from adult male and adult female zebrafish gonad and brain tissue from individuals that had been exposed to atrazine during embryogenesis (GSE72242, GSE72243, GSE73740).
 
Contributor(s) Wirbisky SE, Freeman JL
Citation(s) 28111253
NIH grant(s)
Grant ID Grant title Affiliation Name
R15 ES019137 Molecular biomarkers of exposure to an endocrine disrupting herbicide PURDUE UNIVERSITY Jennifer L Freeman
Submission date Jan 14, 2017
Last update date Aug 11, 2022
Contact name Jennifer Freeman
E-mail(s) jfreema@purdue.edu
Organization name Purdue University
Department School of Health Sciences
Street address 550 Stadium Mall Drive
City West Lafayette
State/province IN
ZIP/Postal code 47907
Country USA
 
Platforms (1)
GPL22921 Agilent-072075 Danio rerio CGH array ZFishCGH_Zv9_Dec2014 G4124A (Feature number version)
Samples (9)
GSM2459292 0.463 um - replicate 1
GSM2459293 4.63 um - replicate 1
GSM2459294 46.3 um - replicate 1
Relations
BioProject PRJNA361362

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

Supplementary file Size Download File type/resource
GSE93635_RAW.tar 394.3 Mb (http)(custom) TAR (of TXT)
GSE93635_adm2_calls_supplementary_file.xlsx 19.3 Kb (ftp)(http) XLSX
Processed data included within Sample table
Processed data are available on Series record

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