|
| Status |
Public on Apr 30, 2014 |
| Title |
LQ-85 |
| Sample type |
genomic |
| |
|
| Source name |
Oral rinse, oral lichenoid disease
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: oral lichenoid disease
Sex: female
cell type: buccal cells
age: 57
tobacco: 0
alcohol: 0
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted and purified from oral rinse samples using the Gentra Puregene Buccal Cell Kit according to standard instructions.
|
| Label |
Cy33
|
| 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.
|
| Data processing |
Quality control and data pre-processing was performed using lumi package (Bioconductor). Samples were background adjusted, processed for the colour channel adjustment 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 |
Jan 17, 2014 |
| 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 |
GPL9183 |
| Series (2) |
| GSE54210 |
Global DNA Methylation: Uncommon Event in Oral Lichenoid Disease [Illumina GoldenGate Methylation Cancer Panel I array] |
| GSE54211 |
Global DNA Methylation: Uncommon Event in Oral Lichenoid Disease |
|
