|
| 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 |
| E-mail(s) |
hs523@cam.ac.uk
|
| 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 |
|
| Relations |
| BioSample |
SAMN02870132 |
| SRA |
SRX620795 |
