|
| Status |
Public on Apr 30, 2014 |
| Title |
LQ-121 |
| Sample type |
genomic |
| |
|
| Source name |
Oral rinse
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
age: 81
disease: Oral Lichenoid disease
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was extracted and purified from oral rinse samples using using Gentra Puregene Buccal Cell Kit according to standard instructions
|
| Label |
Cy3
|
| Label protocol |
standard as recommended by illumina
|
| |
|
| Hybridization protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
LQ-121
|
| Data processing |
Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor).
|
| |
|
| Submission date |
Sep 05, 2013 |
| Last update date |
Apr 30, 2014 |
| Contact name |
Naiara G Bediaga |
| Organization name |
The University of Adelaide
|
| Department |
Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences
|
| Street address |
4 North Terrace
|
| City |
Adelaide |
| State/province |
South Australia |
| ZIP/Postal code |
5000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL8490 |
| Series (2) |
| GSE50608 |
Global DNA methylation: Uncommon event in Oral Lichenoid Disease [Illumina HumanMethylation27 BeadChip] |
| GSE54211 |
Global DNA Methylation: Uncommon Event in Oral Lichenoid Disease |
|
