|
| Status |
Public on Jul 01, 2019 |
| Title |
3V F1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse female germ cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6 background
genotype: Gulo-/-
cell type: female germ cells
age: embryonic day 13.5
treatment: Vitamin C withdrawn
|
| Treatment protocol |
A mouse colony dependent on diet for Vitamin C intake was either supplied with physiological Vitamin C levels or withdrawan from Vitamin C during the first two weeks of gestation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from sorted Oct4+ germ cells by Qiagen RNeasy Micro Kit
1ug total RNA was used in Clonetech SMARTR-seq RNA library prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina HiSeq 4000 reads were trimmed and clipped for quality by trim_galore_v0.4.0 with parameters: --clip_R1 3 --fastqc
High-quality reads were aligned to mm9 genome by TopHat v2.0.13
BAM files were imported into R-Studio and analyzed for differential expression by DESeq2 v1.10.1
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files with RPKM counts normalized for sequencing depth and log transformed.
|
| |
|
| Submission date |
Jan 28, 2018 |
| Last update date |
Jul 01, 2019 |
| Contact name |
Stephanie L Parker |
| E-mail(s) |
slparker87@gmail.com
|
| Organization name |
UCSF
|
| Street address |
35 Medical Center Way
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE109745 |
Maternal Vitamin C regulates DNA demethylation and development of the mouse embryonic germline [RNA-Seq] |
| GSE109747 |
Maternal Vitamin C regulates DNA demethylation and development of the mouse embryonic germline |
|
| Relations |
| BioSample |
SAMN08426381 |
| SRA |
SRX3605592 |
