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Series GSE121585 Query DataSets for GSE121585
Status Public on Jan 19, 2019
Title Developmental Origins of Transgenerational Sperm DNA Methylation Epimutations Following Ancestral DDT Exposure
Organism Rattus norvegicus
Experiment type Methylation profiling by high throughput sequencing
Summary In previous studies, the pesticide DDT was shown to promote the transgenerational inheritance of sperm differential DNA methylation regions (DMRs), also called epimutations, which can mediate this epigenetic inheritance. In the current study, the developmental origins of the transgenerational DMRs during gametogenesis have been investigated. Male control and DDT lineage F3 generation rats were used to isolate embryonic day 16 (E16) prospermatogonia, postnatal day 10 (P10) spermatogonia, adult pachytene spermatocytes, round spermatids, caput epididymal spermatozoa, and caudal sperm. The DMRs between the control versus DDT lineage samples were determined at each developmental stage. The top 100 statistically significant DMRs at each stage were compared and the developmental origins of the caudal epididymal sperm DMRs were assessed.
Overall design F3 generation control and DDT lineage male rats were used in this experimental design to isolate various germ cell stages for epigenetic analysis. The F0 generation gestating female rats at 90 days of age were transiently exposed to DDT or a vehicle control during embryonic days 8-14 when the PGCs were migrating to colonize the indifferent gonad during early stage of gonadal sex determination. The F1 generation offspring were obtained and when they reached 90 days of age they were bred within the control and DDT lineages to generate the F2 generation (grand offspring) which were then bred at 90 days of age to obtain the transgenerational F3 generation for each control and DDT lineage. No cousin or sibling breeding were used to avoid any inbreeding artifacts. Only the F0 generation gestating females were exposed to DDT, which also directly exposed the F1 generation fetus and the germline within the F1 generation fetus that will generate the F2 generation. Therefore, the F3 generation is the first transgenerational generation not directly exposed and was used to study the developmental origins of the sperm epimutations. The F3 generation control and DDT lineage male rats were aged to the embryonic day 16 (E16) fetal stage for prospermatogonia cell isolation, to postnatal day 10 (P10) for spermatogonial cell isolation, and to 120 days of age for pachytene spermatocyte isolation, round spermatid isolation, caput spermatozoa isolation, and cauda epididymal sperm isolation. Three different pools each with different individual sets of animals were obtained from 5-6 males per pool for the E16 stage, 6-7 males per pool for the P10 stage, 3 adult males per pool for the adult stage. Therefore, 3-7 different males were used in the analysis within the three different pools analyzed for both the control and DDT lineages. Genomic DNA was isolated from each pool and from individual animals for caput and cauda sperm for subsequent epigenetic analysis. The analysis of differential DNA methylation regions (DMRs) was performed with a methylated DNA immunoprecipitation (MeDIP) procedure followed by next generation sequencing for an MeDIP-Seq protocol.
Contributor(s) Ben Maamar M, Nilsson E, Sadler-Riggleman I, Beck D, McCarrey JR, Skinner MK
Citation(s) 30500333
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 ES012974 Epigenetic Transgenerational Endocrine Disruptor Actions Washington State University MICHAEL K SKINNER
Submission date Oct 22, 2018
Last update date Apr 22, 2019
Contact name Michael K Skinner
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 (36)
GSM3439691 caput.c1 DDT
GSM3439693 caput.c2 DDT
GSM3439694 caput.c3 DDT
BioProject PRJNA497834
SRA SRP166300

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE121585_Caput.ddt.csv.gz 781.5 Mb (ftp)(http) CSV
GSE121585_Cauda.ddt.csv.gz 733.5 Mb (ftp)(http) CSV
GSE121585_E16.ddt.csv.gz 731.4 Mb (ftp)(http) CSV
GSE121585_P10.ddt.csv.gz 714.8 Mb (ftp)(http) CSV
GSE121585_Pachy.ddt.csv.gz 817.8 Mb (ftp)(http) CSV
GSE121585_RS.ddt.csv.gz 791.3 Mb (ftp)(http) CSV
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