 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 01, 2018 |
| Title |
Developmental Origins of Transgenerational Sperm DNA Methylation Epimutations Following Ancestral Vinclozolin Exposure |
| Organism |
Rattus norvegicus |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
Previously the agricultural fungicide vinclozolin was found to promote the transgenerational inheritance of sperm differential DNA methylation regions (DMRs) termed epimutations that help mediate this epigenetic inheritance. The current study was designed to investigate the developmental origins of the transgenerational DMRs during gametogenesis. Male control and vinclozolin lineage F3 generation rats were used as a source of embryonic day 16 (E16) prospermatogonia, postnatal day 10 (P10) spermatogonia, and adult pachytene spermatocytes, round spermatids, caput epididymal sperm, and caudal sperm. The DMRs between the control versus vinclozolin lineage samples were determined for each developmental stage. The top 100 statistically significant DMRs for each stage were compared and the developmental origins of the caudal epididymal sperm DMRs were assessed.
|
| |
|
| Overall design |
The experimental design involved the development of F3 generation control and vinclozolin lineage male rats to isolate various germ cell stages for epigenetic analysis. The F0 generation gestating female rats at 90 days of age were transiently exposed to vinclozolin or a vehicle control during embryonic days 8–14 when the PGCs were migrating to colonize the indifferent gonad and during the early stages of gonadal sex determination. The F1 generation offspring were obtained and at 90 days of age were bred within the control and vinclozolin lineages, respectively, to generate the F2 generation (grand offspring) which were then bred at 90 days of age to obtain the F3 generation for each control and vinclozolin lineage. No cousin or sibling breedings were used to avoid any inbreeding artifacts. Only the F0 generation gestating females were transiently exposed to vinclozolin, which also directly exposed the F1 generation fetus and the germline within the F1 generation fetus that will generate the F2 generation. Therefore, the transgenerational F3 generation is the first generation not directly exposed and was used to study the developmental origins of the sperm epimutations. The F3 generation control and vinclozolin 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 adult 120 days for pachytene spermatocyte isolation, round spermatid isolation and caput and cauda epididymal sperm isolation. The isolation procedure involved a gravity sedimentation StaPut protocol and direct isolation for the epididymal sperm collections. Three pools each from 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 spermatocyte or spermatid stages, and 3 adult males per pool for the caput or cauda epididymal sperm stages. Therefore, 3-7 different males were used in each of the three different pools analyzed for both the control and vinclozolin lineages. The DNA was isolated from each pool for subsequent epigenetic analysis.
|
| |
|
| Contributor(s) |
Skinner MK, Nilsson E, Sadler-Riggleman I, Beck D, McCarrey JR |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Aug 01, 2018 |
| Last update date |
Nov 01, 2018 |
| 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 (36)
|
|
| Relations |
| BioProject |
PRJNA483950 |
| SRA |
SRP157989 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE117995_Caput.vin.csv.gz |
606.3 Mb |
(ftp)(http) |
CSV |
| GSE117995_Cauda.vin.csv.gz |
675.9 Mb |
(ftp)(http) |
CSV |
| GSE117995_E16.vin.csv.gz |
620.7 Mb |
(ftp)(http) |
CSV |
| GSE117995_P10.vin.csv.gz |
617.2 Mb |
(ftp)(http) |
CSV |
| GSE117995_Pachy.vin.csv.gz |
756.8 Mb |
(ftp)(http) |
CSV |
| GSE117995_RS.vin.csv.gz |
686.3 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...