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Sample GSM1483054 Query DataSets for GSM1483054
Status Public on Sep 01, 2014
Title Whole blood_001-060-002-2010-B
Sample type genomic
Source name whole blood (dried blood spots)
Organism Homo sapiens
Characteristics gender: Female
race: African_american
normalizedpbconc: 3.035195443
age (in months): 12
mother's age (in months): 264
gestational age (in months): 252
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 0.818772396539428
cg00001583 0.0336103962075384
cg00002028 0.0349061648774282
cg00002719 0.0299889010508178
cg00002837 0.395148578666874
cg00003202 0.012264526101606
cg00003287 0.163502169820505
cg00007036 0.96554228920837
cg00007898 0.0130468495105168
cg00008004 0.0575705284736799
cg00008647 0.0987051380919964
cg00009292 0.084734876631598
cg00011717 0.950429073311228
cg00014168 0.742831798151143
cg00015286 0.831248244995299
cg00015930 0.976975162279466
cg00016238 0.906534816869373
cg00017221 0.0454488711393978
cg00017437 0.0560299991458166
cg00021576 0.0379828504290743

Total number of rows: 378548

Table truncated, full table size 10818 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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