|
| Status |
Public on Dec 18, 2018 |
| Title |
Genomic DNA from adult human whole blood [C480341279] |
| Sample type |
genomic |
| |
|
| Source name |
Adult human whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
individual id: X217998019
year of collection: 2014
age: 58
cd8t: 0.0496223484652224
cd4t: 0.168572792404184
nk: 0.0411200725001827
bcell: 0.0286456979972853
mono: 0.105904338810634
gran: 0.628609403425814
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extraction was conducted from buffy coats using QIAamp Blood Mini Kit
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Standard Illumina Protocol
|
| Scan protocol |
Standard Illumina Protocol
|
| Description |
DNA methylation profiling of adult human whole blood (WB)
|
| Data processing |
The methylation signal intensities were generated with minfi Bioconductor package. Functional normalization (e.g., Funnorm) was applied to normalized the between array technical variation. Poor quality samples and probes were excluded based on their detection p-values. The SNP-associated (reported SNPs at the queried CpG site and at the single-base extension (SBE) site) and cross-reactive CpGs were also removed. As we observed statistically significant association between beadchip and the first principal component, we conducted batch-effect correction using ComBat (implemented using the ComBat() function in the sva Bioconductor package).
|
| |
|
| Submission date |
Dec 17, 2018 |
| Last update date |
Dec 18, 2018 |
| Contact name |
Devin Charles Koestler |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Kansas Cancer Center
|
| Department |
Biostatistics
|
| Lab |
the Koestler Lab
|
| Street address |
3901 Rainbow Boulevard
|
| City |
Kansas City |
| State/province |
KS |
| ZIP/Postal code |
66160 |
| Country |
USA |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE123914 |
Variation in DNA methylation of human blood over a 1-year period using the Illumina MethylationEPIC array |
|
