|
| Status |
Public on May 11, 2022 |
| Title |
RNA-seq_E11.5_XX_Control_Rep_2 |
| 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: 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 |
polyA RNA |
| Extraction protocol |
Male and female E11.5 and male E13.5 gonads were extracted and digested in 0.05% trypsin. GFP positive mPGCs were sorted into 300 µL RLT buffer and RNA extracted using the Rneasy Micro Kit (Qiagen)
Following cleanup, the samples were converted to cDNA following the Ovation RNA-seq System V2 protocol (Nugen). cDNA was indexed using the Ovation Rapid DR Multiplex System (Nugen).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
E11_5_female_counts.txt
|
| 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 |
GPL21103 |
| Series (1) |
| GSE139413 |
EED is required for Mouse Primordial Germ Cell Differentiation in the Embryonic Gonad |
|
| Relations |
| BioSample |
SAMN20603775 |
| SRA |
SRX11664967 |
