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Sample GSM1483069 Query DataSets for GSM1483069
Status Public on Sep 01, 2014
Title Whole blood_001-036-005-2009-B
Sample type genomic
Source name whole blood (dried blood spots)
Organism Homo sapiens
Characteristics gender: Male
race: African_american
normalizedpbconc: 5.809591329
age (in months): 36
mother's age (in months): 264
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 0.839753280012006
cg00001583 0.036067591315696
cg00002028 0.0326174754469106
cg00002719 0.0552996473462733
cg00002837 0.381234649006383
cg00003202 0.0122608565202605
cg00003287 0.14815155927712
cg00007036 0.957646531158507
cg00007898 0.0198664351800687
cg00008004 0.0696378975405485
cg00008647 0.0840693046908773
cg00009292 0.0997757546172085
cg00011717 0.95039564477991
cg00014168 0.76367928257134
cg00015286 0.802266179950414
cg00015930 0.971769569047444
cg00016238 0.888173648279197
cg00017221 0.0275991205634113
cg00017437 0.0505669850329235
cg00021576 0.042525104837285

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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