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Title: Comparative high density microarray analysis of global 5hmC patterns in mouse brain and liver following independent affinity based enrichment protocols      
dateReleased:
12-01-2013
description:
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.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-51577
refinement:
raw
alternateIdentifiers:
51577
keywords:
functional genomics
dateModified:
06-03-2014
availability:
available
types:
gene expression
name:
Mus musculus
ID:
A-GEOD-17802
name:
Nimblegen Mouse 2M Tiled Array_2o4 [100205_MM9_Economy_MeDIP_02_HX]
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-51577/E-GEOD-51577.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-51577/E-GEOD-51577.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51577
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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