|
| Status |
Public on Sep 01, 2014 |
| Title |
Whole blood_001-113-002-2012-B |
| Sample type |
genomic |
| |
|
| Source name |
whole blood (dried blood spots)
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
race: African_american
normalizedpbconc: 4.602492159
age (in months): 8.000000004
mother's age (in months): 228
gestational age (in months): 208
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 |
| E-mail(s) |
douglasr@wayne.edu
|
| 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 |
|
