|
| Status |
Public on Nov 05, 2014 |
| Title |
genomic DNA from whole blood_6057825027_R03C01 |
| Sample type |
genomic |
| |
|
| Source name |
whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
450k chip: 6057825027
order on 450k chip: R03C01
gender: Female
tissue: whole blood
disease state: normal
date born: 30-Dec-60
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted and purified from whole blood samples
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
Sample name: X54
normal whole blood sample
|
| Data processing |
BeadStudio softwarewas used to process the raw signal. After the beta values are calculated (Beta value=methylated signal/(methylated signal+unmethylated signal), data quality control was implemented using R (http://www.r-project.org/) (version 2.15.3). We removed 17,764 CpG sites for which probes mapped to multiple loci in the human genome reference sequence. CpG sites that are SNPs, that had missing values, or that had detection p-values >0.01 were excluded. Methylation data from probes mapping to the X and Y chromosomes were excluded. We were left with 394,354 CpG sites from 100 individuals in downstream analyses.
|
| |
|
| Submission date |
Nov 05, 2014 |
| Last update date |
Nov 05, 2014 |
| Contact name |
Weiwei Zhang |
| E-mail(s) |
wz31@duke.edu
|
| Organization name |
Duke University
|
| Department |
Biostatistics and Bioinformatics
|
| Street address |
101 Research Drive
|
| City |
Druham |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE62992 |
Predicting genome-wide DNA methylation |
|
