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Sample GSM1483078 Query DataSets for GSM1483078
Status Public on Sep 01, 2014
Title Whole blood_001-130-001-2007-B
Sample type genomic
Source name whole blood (dried blood spots)
Organism Homo sapiens
Characteristics gender: Male
race: African_american
normalizedpbconc: 7.626344312
age (in months): 48
mother's age (in months): 264
gestational age (in months): 216
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 0.831557614697485
cg00001583 0.0475768650753162
cg00002028 0.0332849653714923
cg00002719 0.0258825661227707
cg00002837 0.421925519229465
cg00003202 0.0152099573211034
cg00003287 0.178624632588597
cg00007036 0.962584296301601
cg00007898 0.0247844297768212
cg00008004 0.0656663822891721
cg00008647 0.101794411765529
cg00009292 0.109548946775433
cg00011717 0.958167365444578
cg00014168 0.729854629560909
cg00015286 0.876508523245246
cg00015930 0.982474900601388
cg00016238 0.957561437321952
cg00017221 0.025190836386697
cg00017437 0.0469595008353819
cg00021576 0.0395636778979602

Total number of rows: 378548

Table truncated, full table size 10810 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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