|
| Status |
Public on May 11, 2022 |
| Title |
WGBS_E11.5_XX_ECKO_Rep_1 |
| Sample type |
SRA |
| |
|
| Source name |
Primordial germ cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Primordial germ cells
strain: C57BL/6;129S1/SvlmJ
developmental stage: E11.5
genotype: Eed -/-
gender: Female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Female E10.5 and E11.5 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 |
Dec 14, 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 |
SAMN24022231 |
| SRA |
SRX13437649 |
