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| Status |
Public on Jul 17, 2019 |
| Title |
Control PND120 sample 16 |
| Sample type |
SRA |
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| Source name |
caudal epididimal sperm
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
tissue: caudal epididimal sperm
postnatal day: 120
exposure: Control
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| Treatment protocol |
Between pregnancy day 8 and postnatal day 21 (PND21) dams were fed daily from the tip of a pipette 0.2 µl/gram body weight of vehicle (tocopherol stripped corn oil, MP Biomedicals, Solon, OH) or same volume of 1 mg/ml solution of BDE-47 (AccuStandard, Inc., New Haven, CT; 100% purity) daily (n=6 per exposure group). In the latter group it resulted in exposure level of 0.2 mg/kg body weight BDE-47 per day.
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| Growth protocol |
Seven-week-old Wistar rats were purchased from Charles River Laboratories (Kingston, NY, USA) on the sixth day of pregnancy, housed in a temperature- and humidity-controlled room with a 12-h light cycle and maintained at 23±2 °C. All rats were fed ad libitum with a rodent chow (Prolab Isopro RMH 3000, Cat. # 5P75, LabDiet, St. Louis, MO).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Upon collection via swim-up procedure, sperm samples were subjected to one-step density gradient centrifugation (40% Isolate, Irvine Scientific, USA) using Eppendorf 5810® centrifuge with bucket rotor A-4-44 and adapter for 15 ml conical tubes to remove somatic cells contamination. DNA was extracted from pellet using the rapid method (Wu H, de Gannes MK, Luchetti G, Pilsner JR. Rapid method for the isolation of mammalian sperm DNA. BioTechniques 2015;58:293-300).
Libraries for RRBS were constructed using 100 ng of epididymal sperm DNA and Ovation RRBS Methyl-Seq System (Cat. # 0353, NuGEN) as per the manufacture’s guidelines. Bisulfte conversion was performed using EpiTect Fast DNA Bisulfite Kit (Cat. # 59824, Qiagen)
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
X9B1
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| Data processing |
mapping by Bismark (version 0.16.1) and bowtie-2 (version 2.2.9)
PCR-duplicates were removed using nudup.py
Differentially methylated regions (DMRs) were identified using MethPipe
DMR spatial annotations using closest-features (v. 2.4.25) tool from bedOps package
Genome_build: rn6
Supplementary_files_format_and_content: xlsx files containing for all significant (q<0.05) DMRs the following information: DMRs' coordinates, number of CpGs per DMR, % change in methylation, nearest gene and distance from gene
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| Submission date |
Jul 16, 2019 |
| Last update date |
Jul 17, 2019 |
| Contact name |
Alexander Suvorov |
| E-mail(s) |
[email protected]
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| Organization name |
University of Massachusetts Amherst
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| Department |
Department of Environmental Health Sciences
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| Street address |
149A - Goessmann, 686 – N. Pleasant Str.
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| City |
Amherst |
| State/province |
MA |
| ZIP/Postal code |
01003 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE134362 |
Changes in rat sperm DNA methylation induced by age and by perinatal exposure to brominated flame retardant flame retardants 2,2’,4,4’-tetrabromodiphenyl ether (BDE-47) |
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| Relations |
| BioSample |
SAMN12284999 |
| SRA |
SRX6451648 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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