Dataset features

Specifications


Application: BS-seq analysis
Number of samples: 9
Release date: Aug 24 2012
Last update date: May 23 2013
Access: Public
Chemicals: 5-Methylcytosine
Dataset link 5-hmC in the brain: abundance in synaptic genes and differences at the exon-intron boundary (MRE-Seq)

Experimental Protocol


The β-glucosyltransferase (BGT) enzyme transfers a glucose molecule specifically to the hydroxymethyl group of 5-hmC, thus rendering it resistant to digestion by the methylation insensitive MspI enzyme at the ChmCGG target site; 5-hmC is thus detected by differential resistance to MspI-digestion with and without glucosylation of genomic DNA (gDNA). HpaII (targets the same site, CCGG) cannot cut CmCGG or ChmCGG, and conceptually its difference with MspI digestion is a measure of both 5-mC and 5-hmC. Subtraction of 5-hmC from the HpaII-based estimate therefore measures 5-mC. These estimates were measured on respective Affymetrix whole-genome tiling arrays (2.0 R ) MspI - APRIL_fc1.ch02_coverage.bed Undigested DNA - APRIL_fc1.ch01_coverage.bed GluMspI - APRIL_fc1.ch04_coverage_NONTARGET.bed GluMspI - APRIL_fc1.ch04_coverage.bed MspI - APRIL_fc1.ch02_coverage_NONTARGET.bed Undigested DNA - APRIL_fc1.ch01_coverage_NONTARGET.bed MspI - MARCH_fc1.ch02_coverage_NONTARGET.bed Undigested DNA - MARCH_fc1.ch01_coverage_NONTARGET.bed GluMspI - MARCH_fc1.ch04_coverage_NONTARGET.bed GluMspI - MARCH_fc1.ch04_coverage.bed MspI - MARCH_fc1.ch02_coverage.bed Undigested DNA - MARCH_fc1.ch01_coverage.bed MspI - MAY_fc1.ch02_coverage.bed GluMspI - MAY_fc1.ch04_coverage_NONTARGET.bed GluMspI - MAY_fc1.ch04_coverage.bed Undigested DNA - MAY_fc1.ch01_coverage.bed MspI - MAY_fc1.ch02_coverage_NONTARGET.bed Undigested DNA - MAY_fc1.ch01_coverage_NONTARGET.bed

Repositories


GEO

GSE40158

ArrayExpress

E-GEOD-40158

ENA

SRP014879

BioProject

PRJNA173641

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Contact


Shraddha Pai

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