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Sample GSM922604 Query DataSets for GSM922604
Status Public on Apr 28, 2012
Title control sperm3
Sample type genomic
 
Channel 1
Source name sperm, control
Organism Homo sapiens
Characteristics cell type: sperm
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 sperm, common reference pool
Organism Homo sapiens
Characteristics cell type: sperm
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 Sperm3 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 -0.089747103
UHNhscpg0000004 0.734283076
UHNhscpg0000005 -0.042197863
UHNhscpg0000006 0.108162001
UHNhscpg0000007 0.096453029
UHNhscpg0000008 -0.052531827
UHNhscpg0000009 0.883685999
UHNhscpg0000011 -0.24161016
UHNhscpg0000012 -0.014586186
UHNhscpg0000013 -0.264364455
UHNhscpg0000017 0.053010338
UHNhscpg0000018 -0.041096081
UHNhscpg0000020 0.114146863
UHNhscpg0000021 0.098232472
UHNhscpg0000022 0.067118793
UHNhscpg0000025 0.331283308
UHNhscpg0000026 0.15937518
UHNhscpg0000029 0.298379091
UHNhscpg0000030 0.003358783
UHNhscpg0000033 -0.082618422

Total number of rows: 8448

Table truncated, full table size 234 Kbytes.




Supplementary file Size Download File type/resource
GSM922604_SP03.gpr.gz 767.0 Kb (ftp)(http) GPR
Processed data included within Sample table

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