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Sample GSM1419028 Query DataSets for GSM1419028
Status Public on Jul 16, 2014
Title meDIP-seq_data_CTRL1
Sample type SRA
Source name Sperm
Organism Mus musculus
Characteristics strain: ICR
antibody: anti-5methyl-cytosine antibody
age: two month
treatment: control dams
Treatment protocol Serial centrifugations were used to purify sperm from potential contaminating cells (such as epithelium or white blood cells).
Growth protocol Sperm was isolated from 2 month old male offspring of control dams or dams undernourished by 50% during the last week of gestation.
Extracted molecule genomic DNA
Extraction protocol Sperm DNA was extracted by standard phenol-chloroform extraction, with an overnight proteinase K reaction at 55 degrees.
DNA was sonicated, paired end adaptors ligated and 12 cycles of whole-genome amplification employed using PhusionTM High-Fidelity Taq and paired end Illumina primers. Libraries were electrophoresed in 2% 1x TAE agarose gels at 95V in 1x TAE buffer followed by excision of a 200bp range band either 200-400bp to 300-500bp according to the peak fragment size. Identical size ranges were obtained for control and UN libraries. qPCR for known methylated and unmethylated regions confirmed library quality.
Library strategy MeDIP-Seq
Library source genomic
Library selection 5-methylcytidine antibody
Instrument model Illumina HiSeq 2000
Data processing preprocessing of the raw reads were performed using FastQC and TrimGalore to remove poor quality bases and adapter sequences
reads post-QC were mapped to mouse reference genome NCBIM37/mm9 using BWA v0.6.2
mapped reads were subject to further QC by SAMtools to remove unmapped, unpaired reads and reads with mapping quality score less than 10
differentially methylated regions (DMRs) were identified using MEDIPS
DNA methylation levels across the whole genome were assessed using sliding windows (size 500bp and 200bp to shift the window)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files, scores represent methylation levels
Submission date Jun 23, 2014
Last update date May 15, 2019
Contact name Hui Shi
Organization name University of Cambridge
Department Department of Physiology, Development and Neuroscience
Street address Downing Street
City Cambridge
ZIP/Postal code CB2 3EG
Country United Kingdom
Platform ID GPL13112
Series (1)
GSE58747 Perturbed adult sperm methylome after in utero undernutrition is associated with transmission of metabolic disease
BioSample SAMN02870132
SRA SRX620795

Supplementary file Size Download File type/resource 105.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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