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Sample GSM1550384 Query DataSets for GSM1550384
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
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
BioSample SAMN03201429
SRA SRX763891

Supplementary file Size Download File type/resource
GSM1550384_rrbsExtr.RRBSIII.131204_ALPACA_64WP2AAXX.setI_high.txt.gz 1.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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