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Sample GSM1483071 Query DataSets for GSM1483071
Status Public on Sep 01, 2014
Title Whole blood_001-045-001-2008-B
Sample type genomic
Source name whole blood (dried blood spots)
Organism Homo sapiens
Characteristics gender: Male
race: African_american
normalizedpbconc: 6.860479927
age (in months): 36
mother's age (in months): 252
gestational age (in months): 216
smoking (0=no, 1=yes): 0
Treatment protocol NA
Extracted molecule genomic DNA
Extraction protocol DNA was isolated from dried blood spots with Qiagen EZ1 Advanced® using the DNA Investigator® reagents and protocol card. The “Stains on Fabric” preprocessing and Trace® (tip-dance) instrument protocol was used for isolation.
Label Cy3, Cy5
Label protocol As described by Illumina for Human methylation 450K assay
Hybridization protocol As described by Illumina for Human methylation 450K assay
Scan protocol As described by Illumina for Human methylation 450K assay
Description Dried blood spots for Pb and DNA methylation study
Data processing Sample normalization done using Bioconductor package ChAMP. Type1 to type 2 probe bias correction was done using Beta mixed interquantile range normalization. Based on gender differences in DNA methylation profile the representative DNA methylation loci was divided into conserved female specific and male specific regions. The CpG sites show highly correlated changes in methylation signatures and can be defined as co-regulated regions. The co-regulated regions were assigned to specified clusters using the A-clustering algorithm (Sofer et al 2013). The association between Pb concentration measured in dried blood spot and DNA methylation of coregulated region for conserved female specific and male specific regions was calculated using Generalized estimating equations (GEE) (Sofer et al 2013)
Rawdata_signal_intensities.txt reports Unmethylated and methylated signal intensities (Pre-normalization)
Submission date Aug 21, 2014
Last update date Sep 01, 2014
Contact name Douglas Ruden
Phone 3135776688
Organization name Wayne State University
Department Department of Obstetrics and Gynecology
Street address 275 E. Hancock Ave., Room 291.1
City Detroit
State/province Michigan
ZIP/Postal code 48201
Country USA
Platform ID GPL13534
Series (1)
GSE60598 Early life Lead exposure causes distinct gender specific changes in the DNA methylation profile of DNA extracted from dried blood spots

Data table header descriptions
VALUE normalized Average Beta

Data table
cg00001349 0.758852366243896
cg00001583 0.0280321609735539
cg00002028 0.0281322141980954
cg00002719 0.0407847593268252
cg00002837 0.342662990694841
cg00003202 0.0123225625415861
cg00003287 0.128346486594441
cg00007036 0.960155322762578
cg00007898 0.0227368380166991
cg00008004 0.0727686864762406
cg00008647 0.0616627717209423
cg00009292 0.0890556697724896
cg00011717 0.961584186073262
cg00014168 0.756147949903868
cg00015286 0.801291722298984
cg00015930 0.978087627591312
cg00016238 0.85249974972245
cg00017221 0.0423547464205486
cg00017437 0.0428963117894387
cg00021576 0.0434225780138793

Total number of rows: 378548

Table truncated, full table size 10815 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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