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Sample GSM922562 Query DataSets for GSM922562
Status Public on Apr 28, 2012
Title control prefrontal cortex33
Sample type genomic
 
Channel 1
Source name prefrontal cortex, control
Organism Homo sapiens
Characteristics tissue: pre-frontal cortex
disease status: control
Extracted molecule genomic DNA
Extraction protocol The samples were first digested using proteinase K (20mg/ml) and lysis buffer mixture at 55°C overnight. A mixture of phenol, chloroform, and iso-amyl alcohol (in ratios of 25:24:1) was used to remove the proteins, followed by two times chloroform wash, precipitation of DNA using cold isopropanol, and a final wash using 70% ethanol. After the extraction, the DNA samples were suspended in 0.1M Tris-EDTA buffer and were kept in -80°C for storage prior to use. The purity and the concentrations of DNA were checked using a UV spectrophotometer (Nanodrop ND1000).
Label Cy5
Label protocol 1 μg of purified enriched PCR products were fluorescently labelled with Cy3 (Roche) for the reference and with Cy5 (Roche) for the sample, as previously described (Schumacher, A., et al. (2006). Microarray-based DNA methylation profiling: technology and applications. Nucleic acids research 34, 528-542.) .
 
Channel 2
Source name prefrontal cortex, common reference pool
Organism Homo sapiens
Characteristics tissue: pre-frontal cortex
sample type: common reference pool
Extracted molecule genomic DNA
Extraction protocol The samples were first digested using proteinase K (20mg/ml) and lysis buffer mixture at 55°C overnight. A mixture of phenol, chloroform, and iso-amyl alcohol (in ratios of 25:24:1) was used to remove the proteins, followed by two times chloroform wash, precipitation of DNA using cold isopropanol, and a final wash using 70% ethanol. After the extraction, the DNA samples were suspended in 0.1M Tris-EDTA buffer and were kept in -80°C for storage prior to use. The purity and the concentrations of DNA were checked using a UV spectrophotometer (Nanodrop ND1000).
Label Cy3
Label protocol 1 μg of purified enriched PCR products were fluorescently labelled with Cy3 (Roche) for the reference and with Cy5 (Roche) for the sample, as previously described (Schumacher, A., et al. (2006). Microarray-based DNA methylation profiling: technology and applications. Nucleic acids research 34, 528-542.) .
 
 
Hybridization protocol The enriched PCR products were hybridized overnight at 48°C onto the 8.1k human CpG island microarray (Microarray Facility, University Health Network, Toronto) as previously described (Schumacher, A., et al. (2006). Microarray-based DNA methylation profiling: technology and applications. Nucleic acids research 34, 528-542.) .
Scan protocol The arrays were scanned using the Genepix 4000B scanner and Genepix Pro 6.0 (Axon Instruments). The automated photomultiplier (PMT) function of the scanner was used to optimize signal intensity and channel balances.
Description Stanley Medical Research Institute prefrontal cortex33 vs. common reference pool
Data processing Linear Models for Microarray Data (LIMMA) package (Bioconductor) for R was used for background correction, normalization, and to extract the signal intensities. Briefly, normexp was used for background correction, print-tip loess was used for within-array normalization, and Gquantile was used for between-array normalization.
 
Submission date Apr 25, 2012
Last update date Apr 28, 2012
Contact name Art Petronis
Organization name Centre for Addiction and Mental Health
Department Campbell Family Mental Health Research Institute
Lab Krembil Family Epigenetics Laboratory
Street address 250 College St
City Toronto
State/province Ontario
ZIP/Postal code M5T1R8
Country Canada
 
Platform ID GPL10342
Series (1)
GSE37579 DNA modification study of major depressive disorder: beyond locus-by-locus comparisons.

Data table header descriptions
ID_REF
VALUE normalized M values where M=log2(Cy5/Cy3)

Data table
ID_REF VALUE
UHNhscpg0000001 0.319808208
UHNhscpg0000004 -0.203527253
UHNhscpg0000005 0.380148713
UHNhscpg0000006 0.123528527
UHNhscpg0000007 0.262774949
UHNhscpg0000008 0.668542753
UHNhscpg0000009 0.001184011
UHNhscpg0000011 -0.081058043
UHNhscpg0000012 0.24214597
UHNhscpg0000013 0.061987588
UHNhscpg0000017 -0.052565927
UHNhscpg0000018 -0.075873718
UHNhscpg0000020 0.567822239
UHNhscpg0000021 -0.269214733
UHNhscpg0000022 -0.175888897
UHNhscpg0000025 0.033815305
UHNhscpg0000026 0.478276823
UHNhscpg0000029 0.18229453
UHNhscpg0000030 0.313890682
UHNhscpg0000033 0.213400961

Total number of rows: 8448

Table truncated, full table size 234 Kbytes.




Supplementary file Size Download File type/resource
GSM922562_CR33.gpr.gz 795.7 Kb (ftp)(http) GPR
Processed data included within Sample table

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