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Sample GSM1483055 Query DataSets for GSM1483055
Status Public on Sep 01, 2014
Title Whole blood_001-084-001-2011-B
Sample type genomic
Source name whole blood (dried blood spots)
Organism Homo sapiens
Characteristics gender: Male
race: African_american
normalizedpbconc: 5.94181757
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 0.741189109709236
cg00001583 0.0329903308164696
cg00002028 0.0245925971134677
cg00002719 0.0492975180355425
cg00002837 0.384843792944579
cg00003202 0.011816085007606
cg00003287 0.129057114095216
cg00007036 0.952204539214251
cg00007898 0.0280305815592983
cg00008004 0.0767320935595493
cg00008647 0.047938602923772
cg00009292 0.0910999590530951
cg00011717 0.947573094354551
cg00014168 0.675025556285476
cg00015286 0.834903509561131
cg00015930 0.980572454475448
cg00016238 0.923918164066294
cg00017221 0.0388754000470307
cg00017437 0.0503773072479996
cg00021576 0.0388849786250674

Total number of rows: 378548

Table truncated, full table size 10816 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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