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Protocols

WAMIDEX specifications

Information


Unique identifier OMICS_15490
Name WAMIDEX
Alternative name Web Atlas of Murine genomic Imprinting and Differential EXpression
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Rodents
    • Mus musculus

Maintainer


  • person_outline Reiner Schulz

Publication for Web Atlas of Murine genomic Imprinting and Differential EXpression

WAMIDEX citations

 (2)
library_books

An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells

2016
eLife
PMCID: 4769179
PMID: 26814573
DOI: 10.7554/eLife.11418.036

[…] ansposon families was calculated and plotted using R. Heatmap for average CpG methylation in Imprinted control regions (ICRs) was generated similarly after retrieving ICR genomic coordinates from the WAMIDEX database (). Residually methylated regions (RMRs) in 2i+vitC samples were identified using the MethPipe pipeline () with default parameters. RMRs located less than 1┬ákb from each others were c […]

call_split

Ontogeny of CpG island methylation and specificity of DNMT3 methyltransferases during embryonic development in the mouse

2014
Genome Biol
PMCID: 4295324
PMID: 25476147
DOI: 10.1186/s13059-014-0545-5
call_split See protocol

[…] s (high CpG promoters), ICPs (intermediate CpG promoters) and LCPs (low CpG promoters) were annotated as previously described []. The genomic coordinates of the imprinted DMRs were retrieved from the Wamidex imprinting database []. The genomic coordinates of canyons were retrieved from a published dataset []. For oocyte methylation, we retrieved a published RRBS dataset (GSE34864) [] and averaged […]


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WAMIDEX funding source(s)
This work was supported by the European Molecular Biology Organization, the Biotechnology and Biological Sciences Research Council and The Wellcome Trust, the Guy's and St. Thomas' Charity, the Agence Nationale pour la Recherche.

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