|
| Status |
Public on Jul 31, 2013 |
| Title |
RNA in the female germ cells at 15.5 dpc |
| Sample type |
SRA |
| |
|
| Source name |
fetal female germ cells at 15.5 dpc
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: CF1 x TgOG2
cell type: germ cells
gender: female
age: 15.5 dpc
|
| Treatment protocol |
N/A
|
| Growth protocol |
in vivo
|
| Extracted molecule |
total RNA |
| Extraction protocol |
GFP+ germ cells and GFP- gonadal somatic cells were flow sorted based on Oct4 promoter-driven EGFP expression in germ cells from CF1XOG2 embryo and fetus gonads using a MoFlo or Aria II flow cytometer. Total RNA was extracted using RNA Bee (Tel Test Inc.). Contaminating DNA was removed with the DNA-free Kit (Ambion). The amount of RNA was monitored using a Nanodrop spectrophotometer followed by a quality check using the Bioanalyzer. All RNA samples had a RIN>9.0. 2µg total RNA samples were depleted for rRNA using the RiboZero Kit (Epicenter, Illumina).
RNA-seq libraries were prepared and paired-end sequencing was performed using the IntegenX RNA kit (Illumina) with read length/coverage of 2x100.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
B_FGC
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).
RNA-seq in the female germ cells at 15.5 dpc.
Strand-specific RNA-Seq.
|
| Data processing |
Illumina Casava 1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v1.2.0 with default settings.
Read counts for each RefSeq gene were summarized using custom built R scripts. The exons in all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the TMM method implemented in Bioconductor package "edgeR" .
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab-delimited text files include normalized read counts for each RefSeq gene.
Supplementary_files_format_and_content: Two bedGraph files (forward and reverse strand separately) for each sample.
|
| |
|
| Submission date |
May 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiwei Wu |
| E-mail(s) |
xwu@coh.org
|
| Organization name |
City of Hope National Medical Center
|
| Department |
Computational and Quantitative Medicine
|
| Street address |
1500 E. Duarte Rd.
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE46953 |
Default DNA Methylation is Preceded by Broad, Low-Level Transcription in Fetal Male Germ Cells and Is Inversely Patterned by Dynamic H3K4 Methylation (RNA-Seq) |
| GSE46954 |
Default DNA Methylation is Preceded by Broad, Low-Level Transcription in Fetal Male Germ Cells and Is Inversely Patterned by Dynamic H3K4 Methylation |
|
| Relations |
| BioSample |
SAMN02144598 |
| SRA |
SRX278424 |
