|
| Status |
Public on Jul 01, 2019 |
| Title |
V1F2 |
| 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treatment: Vitamin C withdrawn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 |
genomic DNA |
| Extraction protocol |
gDNA was extracted from sorted Oct4+ germ cells by PureLink genomic DNA kit.
2ng gDNA was used to create RRBS (reduced representation bisulfite sequencing) libraries. Briefly, gDNA was digested with MspI then repaired with additional A addition. Methylated Illumina adapters were then ligated onto digested gDNA. Adapter ligated DNA was then bisulfite treated using EpiTect Fast Bisulfite Conversion Kit for low-concentration. Finally, libraries were amplified, size selected, and pooled before sequencing on a HiSeq4000.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| 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: --rrbs --fastqc
High-quality reads were aligned to mm9 genome by Bismark v0.14.3 using bowtie2
Methylation calls were extracted from aligned reads by bismark_methylation_extractor
CpG methylation calls were combinded into single bedgraph coverage files with bismark2bedGraph
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files of CpG genomic coordinate, methylation percentage, counts methylated, and counts unmethylated.
|
| |
|
| 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) |
| GSE109746 |
Maternal Vitamin C regulates DNA demethylation and development of the mouse embryonic germline [RRBS] |
| GSE109747 |
Maternal Vitamin C regulates DNA demethylation and development of the mouse embryonic germline |
|
| Relations |
| BioSample |
SAMN08426395 |
| SRA |
SRX3605601 |
