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Sample GSM5504871 Query DataSets for GSM5504871
Status Public on May 11, 2022
Title WGBS_E10.5_XX_Control_Rep_3
Sample type SRA
 
Source name Primordial germ cells
Organism Mus musculus
Characteristics cell type: Primordial germ cells
strain: C57BL/6;129S1/SvlmJ
developmental stage: E10.5
genotype: wild type
gender: Female
Growth protocol Control and ECKO male and female embryos were obtained from crosses between OG; Eedfl/fl (Lengner et al., 2007; Yu et al., 2009) homozygous females and BC; Eedf/l+ heterozygous males (Ohinata et al., 2005) at E10.5, E11.5 and E13.5. Embryos were staged by the detection of a vaginal plug on the morning after time-mating pairs were established E0.5.
Extracted molecule genomic DNA
Extraction protocol Female E10.5 gonads were extracted and digested in 0.05% trypsin. GFP positive single mPGCs were sorted into a 96 well skirtless plate, each well containing 3 µL of 0.2% Triton X-100 and 2U/µL RNaseOUT (Thermo Fisher Scientific).
Cells were sorted into lysis buffer from Zymo MethylDirect Kit and bisulfite converted, and then constructed libraries with Zymo Pico Methylation Kit.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina NovaSeq 6000
 
Data processing The RNA-seq reads were aligned using HISAT2
Genes that are expressed (read counts > 0) in at least one replicate in both control and ECKO are included for analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using edgeR
WGBS reads were aligned with BS Seeker 2. CG sites with read depth >= 4 are preserved in the Cgmap.gz file.
Genome_build: mm9
Supplementary_files_format_and_content: Excel files includes RPKM values for each sample.
 
Submission date Aug 05, 2021
Last update date May 11, 2022
Contact name Pao-Yang Chen
Organization name Academia Sinica
Department Institute of Plant and Microbial Biology
Lab Pao-Yang Chen
Street address 128 Sec. 2, Academia Rd, Nankang,
City Taipei
ZIP/Postal code 115
Country Taiwan
 
Platform ID GPL24247
Series (1)
GSE139413 EED is required for Mouse Primordial Germ Cell Differentiation in the Embryonic Gonad
Relations
BioSample SAMN20603817
SRA SRX11664994

Supplementary file Size Download File type/resource
GSM5504871_E284-3-WT-4--E10dot5-E284-3-Female-WGBS-Control-4-4X_CG.CGmap.gz 61.1 Mb (ftp)(http) CGMAP
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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