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Sample GSM7220318 Query DataSets for GSM7220318
Status Public on Jun 07, 2023
Title Male_low
Sample type SRA
 
Source name embryonic gonad
Organism Mus musculus
Characteristics tissue: embryonic gonad
strain: OG2
generation: F3
cell type: primordial germ cell
Sex: M
treatment: Exposed to 0.033 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 SAMN34314223
SRA SRX20063659

Supplementary file Size Download File type/resource
GSM7220318_Male_low_F3.bedGraph.gz 149.3 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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