|
| Status |
Public on Mar 16, 2021 |
| Title |
LP14: no disease |
| Sample type |
SRA |
| |
|
| Source name |
no disease
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
Sex: male
tissue: Sperm
measurement: MeDIP
disease: no disease
lineage: plastics
|
| Treatment protocol |
Outbred Sprague Dawley gestating female rats (F0 generation) were administered an intraperitoneal dose of the plastic compound mixture (BPA 25 mg/kg BW/day, DEHP 375 mg/kg BW /day, and DBP 33mg/kg BW/day). These doses were administered at 90 days of age, during embryonic days 8-14 (E8-E14) of fetal gonadal sex determination. The F1 generation offspring was directly exposed as a fetus and F2 generation grand-offspring exposed as the germline in the F1 generation. These were each bred at 90 days of age within the lineage. The F3 generation great-grand-offspring is required to establish the transgenerational inheritance generation of ancestral exposure.
|
| Growth protocol |
Female and male rats of an outbred strain Hsd:Sprague Dawley SD (Harlan) at 70 to 100 days of age were fed ad lib with a standard rat diet and ad lib tap water. The gestating female rats treated were designated as the F0 generation. F1- F3 generation plastics lineages were housed in the same room and racks with lighting, food and water. All experimental protocols for the procedures with rats were pre-approved by the Washington State University Animal Care and Use Committee (protocol IACUC # 6252).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
See attached Word document (Extraction_Library_Construction_Protocol.docx)
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs, the reference genome was broken into 1000 bp windows. Genomic windows with a mean of less than 10 mapped reads per sample were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between disease and non-disease sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than an arbitrarily selected threshold were considered DMRs. The DMR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.
|
| |
|
| Submission date |
Dec 17, 2020 |
| Last update date |
Mar 16, 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 |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE163412 |
Ancestral Plastics Exposure Induces Transgenerational Disease Specific Sperm Epigenome-Wide Association Biomarkers Methylation Epimutation Biomarkers for Specific Transgenerational Disease |
|
| Relations |
| BioSample |
SAMN17103529 |
| SRA |
SRX9697653 |
