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Sample GSM1483060 Query DataSets for GSM1483060
Status Public on Sep 01, 2014
Title Whole blood_001-085-002-2011-B
Sample type genomic
Source name whole blood (dried blood spots)
Organism Homo sapiens
Characteristics gender: Female
race: African_american
normalizedpbconc: 25.59618366
age (in months): 12
mother's age (in months): 240
gestational age (in months): 228
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 0.850880653710676
cg00001583 0.0270830354576465
cg00002028 0.0369107373364051
cg00002719 0.0294772017135023
cg00002837 0.451279094941471
cg00003202 0.0132204342499931
cg00003287 0.147882533445237
cg00007036 0.961032250665634
cg00007898 0.0199589129793539
cg00008004 0.0583185510853465
cg00008647 0.0693338920058598
cg00009292 0.0881539837692366
cg00011717 0.952537477227524
cg00014168 0.703461528692882
cg00015286 0.853190266166878
cg00015930 0.980305534799246
cg00016238 0.891107229821893
cg00017221 0.0241672761602361
cg00017437 0.0494840255729705
cg00021576 0.0354675046939267

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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