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Sample GSM1483065 Query DataSets for GSM1483065
Status Public on Sep 01, 2014
Title Whole blood_001-087-002-2010-B
Sample type genomic
Source name whole blood (dried blood spots)
Organism Homo sapiens
Characteristics gender: Female
race: African_american
normalizedpbconc: 2.938008435
age (in months): 24
mother's age (in months): 252
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 0.792044731472478
cg00001583 0.0279957159526227
cg00002028 0.0356231009490359
cg00002719 0.0211190241806106
cg00002837 0.433654337327037
cg00003202 0.0110546144731452
cg00003287 0.184157079119783
cg00007036 0.967256706659026
cg00007898 0.0248876454278328
cg00008004 0.0629567555465078
cg00008647 0.0604510490327873
cg00009292 0.0999077889171993
cg00011717 0.950972692403186
cg00014168 0.692506574783196
cg00015286 0.824606239461714
cg00015930 0.976452676572939
cg00016238 0.9402786024821
cg00017221 0.0436676866366786
cg00017437 0.0521787597606196
cg00021576 0.0299515771098326

Total number of rows: 378548

Table truncated, full table size 10817 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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