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Series GSE106125 Query DataSets for GSE106125
Status Public on Jan 12, 2018
Title Epigenetic Transgenerational Inheritance of Altered Sperm Histone Retention Sites
Organism Rattus norvegicus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Female and male rats of an outbred female Sprague Dawley rats were administered daily intraperitoneal injections of vinclozolin (100 mg/kg BW/day), or DDT (25 mg/kg BW/day) or dimethyl sulfoxide (DMSO) in oil (1 µl/kg BW/day vehicle). Treatment lineages are designated “control” or “vinclozolin” or “DDT” lineages. The gestating female rats treated were designated as the F0 generation. The offspring of the F0 generation rats were the F1. Non-littermate females and males aged 70-90 days from F1 generation of control, vinclozolin or DDT were bred to obtain F2 generation offspring. The F2 generation rats were similarly bred to obtain the F3 generation offspring. Individuals were maintained for 120 days and euthanized for sperm collection. Sperm from multiple individual rats was pooled into single samples. For the control samples, 2 pools were made using 6 animals and 1 pool with 5 animals. For the DDT samples, 3 pools were mady using 4 animals. For the Vinclozolin samples, 3 pools were made using 4 animals. Genomic DNA was isolated and histone chromatin immunoprecipitation with genomic DNA was performed. Each pooled sample received a separate index primer. NGS was performed at the WSU Spokane Genomics Core using Ilumina HiSeq 2500 with a PE50 application, with a read size of approximately 50 bp and approximately 35 million reads per pool.
 
Overall design Female rats were administered daily intraperitoneal injections of vinclozolin (100 mg/kg BW/day), or DDT (25 mg/kg BW/day) or dimethyl sulfoxide (DMSO) in oil (1 µl/kg BW/day vehicle). Vinclozolin and DDT (dichlorodiphenyltrichloroethane) were obtained from Chem Service Inc. (West Chester, PA). Vinclozolin and DDT were injected in DMSO vehicle. Treatment lineages are designated “control” or “vinclozolin” or “DDT” lineages. The gestating female rats treated were designated as the F0 generation. The offspring of the F0 generation rats were the F1. Non-littermate females and males aged 70-90 days from F1 generation of control, vinclozolin or DDT were bred to obtain F2 generation offspring. The F2 generation rats were similarly bred to obtain the F3 generation offspring. Individuals were maintained for 120 days and euthanized for sperm collection and sample processing. Both DDT and vinclozolin samples were seperately compared to the DMSO control samples.
 
Contributor(s) Ben Maamar M, Sadler-Riggleman I, Beck D, Skinner MK
Citation(s) 29482626
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 24, 2017
Last update date May 15, 2019
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 (23)
GSM2830099 Vinc1.P16
GSM2830100 Vinc2.P17
GSM2830101 Vinc3.P18
Relations
BioProject PRJNA415641
SRA SRP121352

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
GSE106125_F3.DDT.results.csv.gz 1.2 Gb (ftp)(http) CSV
GSE106125_F3.Vin.results.csv.gz 1.0 Gb (ftp)(http) CSV
GSE106125_F3me.DDT.results.csv.gz 601.0 Mb (ftp)(http) CSV
GSE106125_five.rats.results.csv.gz 358.8 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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