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Series GSE156530 Query DataSets for GSE156530
Status Public on Nov 19, 2020
Title Epigenome-Wide Association Study for Atrazine Induced Transgenerational Histone Retention Sperm Epigenetic Biomarkers for Disease
Organism Rattus norvegicus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Atrazine is a common agricultural herbicide previously shown to promote epigenetic transgenerational inheritance of disease to subsequent generations. The current study was designed as an epigenome-wide association study (EWAS) to identify transgenerational sperm disease associated differential histone retention regions (DHRs). Gestating female F0 generation rats were transiently exposed to atrazine during the period of embryonic gonadal sex determination, and then subsequent F1, F2, and F3 generations obtained in the absence of any continued exposure. The transgenerational F3 generation males were assessed for disease and sperm collected for epigenetic analysis. Pathology was observed in late pubertal onset and for testis disease, prostate disease, kidney disease, lean pathology, and multiple disease. For these pathologies, sufficient numbers of individual males with only a single specific disease were identified. The sperm DNA and chromatin were isolated from adult one-year animals with the specific diseases and analyzed for DHRs with histone chromatin immunoprecipitation (ChIP) sequencing. Transgenerational F3 generation males with or without disease were compared to identify the disease specific epimutation biomarkers. No common DHRs were found among all the pathologies. Epimutation gene associations were identified and found to correlate to previously known disease linked genes.
 
Overall design Analysis of the transgenerational actions of atrazine used outbred Sprague Dawley female rats (F0 generation) transiently exposed (25 mg/kg body weight atrazine daily) during days 8 to 14 of gestation. The F1 generation animals (direct fetal exposure) were bred to generate the F2 generation (direct germline exposure), which were bred to generate the F3 generation (transgenerational so no direct exposure). A control lineage used F0 generation gestating females administered vehicle control dimethyl sulfoxide (DMSO). The control and atrazine lineages were aged to 1 year and euthanized for pathology and sperm epigenetic analysis. No sibling or cousin breedings (crosses) were used to avoid any inbreeding artifacts in either the control or atrazine lineages. Generally 6–8 founder gestating females from different litters were bred and 25–50 individuals of each sex obtained for each generation.
Web link https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0239380
 
Contributor(s) Thorson JL, Beck D, Maamar MB, Nilsson E, Margaux M, Skinner MK
Citation(s) 33326428
Submission date Aug 20, 2020
Last update date Feb 18, 2021
Contact name Michael K Skinner
E-mail(s) skinner@mail.wsu.edu
Organization name WSU
Department SBS
Street address Abelson 507
City Pullman
State/province WA
ZIP/Postal code 99163
Country USA
 
Platforms (1)
GPL18694 Illumina HiSeq 2500 (Rattus norvegicus)
Samples (67)
GSM4732988 M1_Sperm_Control_ChIP
GSM4732989 M2_Sperm_Control_ChIP
GSM4732990 M3_Sperm_Control_ChIP
Relations
BioProject PRJNA658259
SRA SRP278178

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
GSE156530_exposure.dhr.results.csv.gz 513.6 Mb (ftp)(http) CSV
GSE156530_kidney.dhr.results.csv.gz 230.4 Mb (ftp)(http) CSV
GSE156530_latepuberty.dhr.results.csv.gz 237.8 Mb (ftp)(http) CSV
GSE156530_lean.dhr.results.csv.gz 258.0 Mb (ftp)(http) CSV
GSE156530_multiple.dhr.results.csv.gz 307.4 Mb (ftp)(http) CSV
GSE156530_testis.dhr.results.csv.gz 232.8 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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