Transcriptomics

Dataset Information

8

Comparative high density microarray analysis of global 5hmC patterns in mouse brain and liver following independent affinity based enrichment protocols.


ABSTRACT: On mouse tiled microarrays (GPL17802), we profile 5hmC in WT mouse livers and brains following fragment enrichment by one of three affinity based techniques: i- antibody (HmeDIP), ii- Chemical capture (hMeSeal) and iii-JBP-1 protein affinity (JBP). HmeDIP and hMeSeal both return similar patterns of 5hmC whilst JBP enriched patterns (carriedo out on brain only) resemble background noise. 5hmC is largely found to reside in the bodies of active genes as well as being enriched over enhancer and promoter proximal regions. WT C57BL/6 mice aged 30-32 days old at time of organ removal. Tissues taken and frozen in liquid nitrogen prior to DNA extraction. Genomic DNA was sonicated (Bioruptor, Diagenode) to produce DNA fragments ranging in size from 200 to 1,000 bp, with a mean fragment size of around 300 bp. i- HmeDIP: antibody enrichment carried out as previously reported by Thomson et al 2013 (doi:10.1093/nar/gkt232). ii- HmeSeal: Enrichment based on the hMe-Seal based techniques described by Song et al 2010 (doi: 10.1038/nbt.1732) and marketed by Active motif under the name hydroxymethyl-collector kit. iii- JBP-1 affinity purification: Enrichment carried out using the Quest 5hmC DNA enrichment kit marketed by Zymo research.

ORGANISM(S): Mus musculus  

SUBMITTER: Richard R Meehan   John Paterson Thomson  John P Thomson  Jennifer M Hunter 

PROVIDER: E-GEOD-51577 | ArrayExpress | 2013-12-01

SECONDARY ACCESSION(S): GSE51577PRJNA223533

REPOSITORIES: GEO, ArrayExpress

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Publications

Dynamic changes in 5-hydroxymethylation signatures underpin early and late events in drug exposed liver.

Thomson John P JP   Hunter Jennifer M JM   Lempiäinen Harri H   Müller Arne A   Terranova Rémi R   Moggs Jonathan G JG   Meehan Richard R RR  

Nucleic acids research 20130417 11


Aberrant DNA methylation is a common feature of neoplastic lesions, and early detection of such changes may provide powerful mechanistic insights and biomarkers for carcinogenesis. Here, we investigate dynamic changes in the mouse liver DNA methylome associated with short (1 day) and prolonged (7, 28 and 91 days) exposure to the rodent liver non-genotoxic carcinogen, phenobarbital (PB). We find that the distribution of 5mC/5hmC is highly consistent between untreated individuals of a similar age;  ...[more]

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