|
| Status |
Public on Jun 07, 2023 |
| Title |
Female_high |
| Sample type |
SRA |
| |
|
| Source name |
embryonic gonad
|
| Organism |
Mus musculus |
| Characteristics |
tissue: embryonic gonad
strain: OG2
generation: F3
cell type: primordial germ cell
Sex: F
treatment: Exposed to 2 mg/kg/day BaP
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from FACS-enriched mouse primordial germ cells (20,000 - 30,000 cells) using AllPrep Micro Kit (QIAGEN) and subjected to bisulfite conversion using EZ DNA Methylation-Gold Kit (Zymo Research) following manurfacturers' instructions.
Illumina libraries were synthesized using Accel-NGS Methyl-seq DNA Library Kit (Swift Biosciences) following manufacturer's instructions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired-end (150 + 150) FASTQ files were subjected to trimGalore pre-processing to remove Illumina adaptor sequences and low quality reads (Q<30).
Trimmed FASTQ files were analyzed using the Bismark toolkit to examine CpG methylation. Bismark aligned FASTQ data to the mm10 mouse reference genome using Bowtie2.
Bismark generated .begGraph files reporting CpG site coordinates and their degree of DNA methylation (0-100%).
CpG sites were classified based on their degree of methylation and linked to known mouse repetitive sequences registered in the RepeatMasker file of mm10.
Assembly: mm10
Supplementary files format and content: BedGraph files include coordinates and methylation of CpG sites.
|
| |
|
| Submission date |
Apr 22, 2023 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Toshi Shioda |
| E-mail(s) |
tshioda@partners.org
|
| Phone |
(617) 726-3425
|
| Organization name |
MGH Cancer Center
|
| Department |
Center for Cancer Research
|
| Lab |
Molecular Profiling Lab
|
| Street address |
Building 149 - 7th Floor, 13th Street
|
| City |
Charlestown |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE230356 |
Prenatal exposure to benzo[a]pyrene depletes ovarian reserve and masculinizes embryonic ovarian germ cell transcriptome transgenerationally [Bisulfite-Seq] |
|
| Relations |
| BioSample |
SAMN34314227 |
| SRA |
SRX20063655 |
