|
| Status |
Public on Feb 01, 2014 |
| Title |
Chimpanzee_MeDIP |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Pan troglodytes |
| Characteristics |
tissue: blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MagMeDIP kit (Diagenode) for Immunoprecipitation
Pooled DNA from these samples was subjected to AutoMeDIP-seq as previously described (Butcher et al. Methods (2010) 52, 223-31), using the NEBNext DNA Sample Prep Mastermix (New England Biolabs) for the library preparation and the MagMeDIP kit (Diagenode) for the immunoprecipitation. Adequate enrichment of the methylated DNA fraction (compared to input) was quality controlled using qPCR. Following adapter-mediated PCR, the library was subjected to size selection (300-350 bp) from low melting-point agarose gels. The excised fraction was quality controlled by qPCR. Cluster generation and 36 base paired-end sequencing was performed by the UCL Genomics Core Facility according to the manufacturer’s recommendation, using an Illumina GAIIX platform.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
DNA IP against 5-Methylcytosine
|
| Data processing |
Alignment was performed using BWA v0.5.8 with default parameters
Filtering was performed using SAMtools to remove reads with low alignment score. Only those forming a correctly aligned pair were kept. A final filtering step removed potential PCR artefacts by discarding all but one read-pair within groups of non-unique fragments.
Aligned fragments were lifted from the host genome to hg19
Wig files were created using the MEDIPS v1.0 bioconductor package
Genome_build: hg19, panTro2.1, mmul1
Supplementary_files_format_and_content: Bigwig files generated by converting wig files generated in MEDIPS using wigToBigWig from UCSC. Scores represent normalised (reads per million) read depth across the genome. Bed files contain lists of differentially methylated regions located in the human genome (hg19). These were defined by comparison of human MeDIP-seq data to chimpanzee (panTro2) and macaque (rheMac2) MeDIP-seq data.
|
| |
|
| Submission date |
Jul 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gareth Wilson |
| E-mail(s) |
gareth.wilson@ucl.ac.uk
|
| Organization name |
UCL Cancer Institute
|
| Street address |
23 Huntley Street
|
| City |
London |
| ZIP/Postal code |
WC1E 6BT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9378 |
| Series (1) |
| GSE48942 |
Compararitve Triprimate Peripheral Blood DNA Methylome |
|
| Relations |
| BioSample |
SAMN02254954 |
| SRA |
SRX323420 |
