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E-GEOD-67188 - The alteration of 5-hydroxymethylcytosine modification contributes to ischemic brain injury [5hmC-seq]

Status
Released on 8 September 2015, last updated on 12 September 2015
Organism
Mus musculus
Samples (6)
Protocols (1)
Description
Epigenetic modifications, such as cytosine methylation and histone modification, have been shown involved in the pathology of ischemic brain injury. Recent works have implicated 5-hydroxymethylcytosine (5hmC), a DNA base derived from 5-methylcytosine (5mC) through the oxidation by Ten-Eleven Translocation (TET) enzymes, in DNA methylation-related plasticity. In this study we show that 5hmC abundance could be induced to increase by ischemia injury. Genome-wide profiling of 5hmC identified differentially hydroxymethylated regions (DhMRs) associated with ischemic injury and DhMRs were found enriched among the genes involved in cell junction, neuronal morphogenesis and neurodevelopment. These data together suggest that 5hmC modification could serve as a potential therapeutic target for the treatment of ischemic stroke. To determine the genome-wide 5hmC distribution in both ischemic injury (I/R) and control mice (C57BL/6), we employed a previously established chemical labeling and affinity purification method, coupled with high-throughput sequencing (Song et al, Nature Biotechnology, 2011). The ischemic or matched control brain tissues from three pairs of ischemic mice and control mice were used for the analyses.
Experiment type
methylation profiling by high throughput sequencing 
Contacts
Peng Jin, Xingshun Xu
Citation
Altering 5-hydroxymethylcytosine modification impacts ischemic brain injury. Miao Z, He Y, Xin N, Sun M, Chen L, Lin L, Li J, Kong J, Jin P, Xu X.
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-67188.idf.txt
Sample and data relationshipE-GEOD-67188.sdrf.txt
Additional data (1)E-GEOD-67188.additional.1.zip
Links