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Sample GSM1483052 Query DataSets for GSM1483052
Status Public on Sep 01, 2014
Title Whole blood_001-051-001-2011-B
Sample type genomic
Source name whole blood (dried blood spots)
Organism Homo sapiens
Characteristics gender: Male
race: African_american
normalizedpbconc: 2.27245527
age (in months): 12
mother's age (in months): 216
gestational age (in months): 204
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 0.838158862912734
cg00001583 0.0296709270389107
cg00002028 0.0241628203836224
cg00002719 0.0256997612348584
cg00002837 0.404020692845116
cg00003202 0.0101597290013522
cg00003287 0.16742007193331
cg00007036 0.952046299537779
cg00007898 0.0161066286602536
cg00008004 0.0563162446754691
cg00008647 0.0890512138668912
cg00009292 0.0962126024956355
cg00011717 0.944797144903926
cg00014168 0.697832549135678
cg00015286 0.817065176659149
cg00015930 0.971361825493663
cg00016238 0.931823075338541
cg00017221 0.0355844633860946
cg00017437 0.0473767541264948
cg00021576 0.0379574501601739

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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