|
| Status |
Public on Oct 14, 2015 |
| Title |
young set1_RRBS |
| Sample type |
SRA |
| |
|
| Source name |
young set_RRBS
|
| Organism |
Homo sapiens |
| Characteristics |
age group: young
cell type: ovarian granulosa cells
molecule subtype: Bisulfite treated DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ovarian granulosa cells were purified from follicular fluids obtained at the time of oocyte retrieval. DNA was extracted QIAamp DNA mini kits (Qiagen).
MethylCap-seq (PMID:20852634; 20542119) and RRBS libraries (PMID: 21412275; 23325432) were prepared according to protocols previously published.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
young set1
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then MethylCap reads were mapped to hg19 whole genome using bowtie
Bismark was used for read mapping and methylation calling in RRBS datasets.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include peak values (in MethylCap-seq datasets) or methylation levels (in RRBS datasets) for each set of samples (young versus old). MethylCap-seq data: used sliding window of 2000bp and 1000bp step.
|
| |
|
| Submission date |
Nov 19, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Bo Yu |
| E-mail(s) |
boyumich2@gmail.com
|
| Organization name |
Albert Einstein College of Medicine
|
| Street address |
1300 Morris Park Ave, Block 621
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE63470 |
Human ovarian granulosa cell methylome |
|
| Relations |
| BioSample |
SAMN03201429 |
| SRA |
SRX763891 |
