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Sample GSM1483050 Query DataSets for GSM1483050
Status Public on Sep 01, 2014
Title Whole blood_001-122-002-2011-B
Sample type genomic
Source name whole blood (dried blood spots)
Organism Homo sapiens
Characteristics gender: Female
race: African_american
normalizedpbconc: 1.972338713
age (in months): 12
mother's age (in months): 240
gestational age (in months): 228
smoking (0=no, 1=yes): 1
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 0.818269541638926
cg00001583 0.0351368605949771
cg00002028 0.0260757612718152
cg00002719 0.0324552961461396
cg00002837 0.48262303040105
cg00003202 0.015714385911384
cg00003287 0.178302042643679
cg00007036 0.958498636280401
cg00007898 0.0236665206073098
cg00008004 0.0740546541238918
cg00008647 0.100238776757926
cg00009292 0.106314322169591
cg00011717 0.945401858847203
cg00014168 0.673091489361957
cg00015286 0.827907012323311
cg00015930 0.977532186927601
cg00016238 0.914983221692948
cg00017221 0.0572632302964484
cg00017437 0.050996683259214
cg00021576 0.0299762103926852

Total number of rows: 378548

Table truncated, full table size 10813 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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