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| Status |
Public on Feb 05, 2011 |
| Title |
[E-TABM-482] DNA methylome of human spermatozoa |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Genome-wide DNA methylation profile of human spermatozoa using the meDIP technique and massively parallel sequencing.
DNA methylation is an indispensible epigenetic modification required for regulating the expression of mammalian genomes. Immunoprecipitation-based methods for DNA methylome analysis are rapidly shifting the bottleneck in this field from data generation to data analysis, necessitating the development of better analytical tools. In particular, an inability to estimate absolute methylation levels remains a major analytical difficulty associated with immunoprecipitation-based DNA methylation profiling. To address this issue, we developed a cross-platform algorithm-Bayesian tool for methylation analysis (Batman)-for analyzing methylated DNA immunoprecipitation (MeDIP) profiles generated using oligonucleotide arrays (MeDIP-chip) or next-generation sequencing (MeDIP-seq). We developed the latter approach to provide a high-resolution whole-genome DNA methylation profile (DNA methylome) of a mammalian genome. Strong correlation of our data, obtained using mature human spermatozoa, with those obtained using bisulfite sequencing suggest that combining MeDIP-seq or MeDIP-chip with Batman provides a robust, quantitative and cost-effective functional genomic strategy for elucidating the function of DNA methylation.
ArrayExpress Release Date: 2008-06-10
Publication Title: A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
Publication Author List: Thomas A Down; Vardhman K Rakyan; Daniel J Turner; Paul Flicek; Heng Li; Eugene Kulesha; Stefan Gräf; Nathan Johnson; Javier Herrero; Eleni M Tomazou; Natalie P Thorne; Liselotte Bäckdahl; Marlis Herberth; Kevin L Howe; David K Jackson; Marcos M Miretti; John C Marioni; Ewan Birney; Tim J P Hubbard; Richard Durbin; Simon Tavaré; Stephan Beck
Person Roles: submitter; investigator
Person Last Name: Flicek
Person First Name: Paul
Person Mid Initial
Person Email: flicek@ebi.ac.uk
Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Person Affiliation: European Bioinformatics Institute
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| Overall design |
Experimental Design: high_throughput_sequencing_design
Experimental Factor Name: CELLTYPE
Experimental Factor Type: cell_type
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| Citation(s) |
18612301 |
| Submission date |
Nov 29, 2010 |
| Last update date |
Feb 21, 2019 |
| Organization |
European Bioinformatics Institute |
| E-mail(s) |
miamexpress@ebi.ac.uk
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| Lab |
ArrayExpress
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| Street address |
Wellcome Trust Genome Campus
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| City |
Hinxton |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB10 1SD |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
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| Samples (1) |
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| Relations |
| ArrayExpress |
E-TABM-482 |
| BioProject |
PRJNA135835 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE25686_RAW.tar |
61.9 Mb |
(http)(custom) |
TAR (of GFF) |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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