NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM922374 Query DataSets for GSM922374
Status Public on Apr 28, 2012
Title Australian Twin Registry monozygotic twin23a control white blood cells45
Sample type genomic
 
Channel 1
Source name white blood cells, control
Organism Homo sapiens
Characteristics cell type: white blood cells
disease status: control
individual: Australian Twin Registry monozygotic twin23a
twin pair: twin23
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 white blood cells, common reference pool
Organism Homo sapiens
Characteristics cell type: white blood cells
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 Australian Twin Registry monozygotic twin23a 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 0.316762501
UHNhscpg0000004 0.240917263
UHNhscpg0000005 0.03849987
UHNhscpg0000006 0.244328052
UHNhscpg0000007 0.162035763
UHNhscpg0000008 0.13330001
UHNhscpg0000009 0.317159798
UHNhscpg0000011 -0.069704633
UHNhscpg0000012 0.136125747
UHNhscpg0000013 0.174711255
UHNhscpg0000017 -0.024907124
UHNhscpg0000018 0.082133137
UHNhscpg0000020 -0.078242745
UHNhscpg0000021 0.060292863
UHNhscpg0000022 0.14857182
UHNhscpg0000025 0.252986444
UHNhscpg0000026 0.018217486
UHNhscpg0000029 -0.026540185
UHNhscpg0000030 -0.182790818
UHNhscpg0000033 0.055811885

Total number of rows: 8448

Table truncated, full table size 234 Kbytes.




Supplementary file Size Download File type/resource
GSM922374_AU45.gpr.gz 721.8 Kb (ftp)(http) GPR
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap