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Sample GSM587828 Query DataSets for GSM587828
Status Public on Aug 28, 2010
Title 432_brain_normal
Sample type genomic
 
Channel 1
Source name Input fraction from normal brain
Organism Homo sapiens
Characteristics sample type: Input fraction from normal brain
tissue: frontal cortex
Treatment protocol untreated
Growth protocol genomic DNA was isolated from frozen tissue, i.e. not grown in culture
Extracted molecule genomic DNA
Extraction protocol Genomic DNA (gDNA) were isolated using the MasterPure genomic DNA isolation kit (EpiCentre) according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was randomly sheared into 1.6-3kb DNA size fragments using a Hydroshear device (DigiLab), digested with McrBC, and fractionated on a 1% agarose gel alongside the sheared input (UT) fraction to enrich for the unmethylated (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.
Label Cy3
Label protocol 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).
 
Channel 2
Source name Methyl-depleted fraction from normal brain
Organism Homo sapiens
Characteristics tissue: frontal cortex
sample type: Methyl-depleted fraction from normal brain
Treatment protocol untreated
Growth protocol genomic DNA was isolated from frozen tissue, i.e. not grown in culture
Extracted molecule genomic DNA
Extraction protocol Genomic DNA (gDNA) were isolated using the MasterPure genomic DNA isolation kit (EpiCentre) according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was randomly sheared into 1.6-3kb DNA size fragments using a Hydroshear device (DigiLab), digested with McrBC, and fractionated on a 1% agarose gel alongside the sheared input (UT) fraction to enrich for the unmethylated (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.
Label Cy5
Label protocol 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).
 
 
Hybridization protocol The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).
Scan protocol Arrays were scanned on a GenePix 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).
Description DNA methylation data from human brain
Data processing Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 software and the charm bioconductor package v1.0.1 using a) quantile and b) subset-quantile normalization. Percent methylation calculated.
 
Submission date Aug 27, 2010
Last update date Aug 27, 2010
Contact name Martin Aryee
E-mail(s) Martin.aryee@ds.dfci.harvard.edu
Organization name Massachusetts General Hospital
Department Pathology
Street address 149 13th Street
City Charlestown
State/province MA
ZIP/Postal code 02129
Country USA
 
Platform ID GPL9275
Series (1)
GSE23841 DNA methylation data from human liver, frontal cortex, spleen and colon

Supplementary file Size Download File type/resource
GSM587828_136726_532.xys.gz 10.4 Mb (ftp)(http) XYS
GSM587828_136726_635.xys.gz 10.5 Mb (ftp)(http) XYS
Processed data are available on Series record

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