|
| Status |
Public on Feb 25, 2014 |
| Title |
lung_non-malignant_DNA (85040002): MP |
| Sample type |
genomic |
| |
|
| Source name |
lung, non-malignant
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: control
sample number: 85040002
|
| Growth protocol |
Tissues were excised during surgical ressection for tumor removal.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumour and normal samples were obtained during surgical ressection. After pathology review, tumors were microdissected to ensure tumor cells comprised 80% of cells extracted. DNA was extracted using proteinase K digestion, followed by phenol:chloroform extraction and ethanol precipitation.
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Bisulfite conversion and labelling was carried out according to Illumina directions by the Illumina Cspro service center at Oxford University.
Bisulfite conversion leads to the deamination of non-methylated cytosines to uracils, while methylated cytosines are refractory to the effects of bisulfite and remain cytosine.
Methylated alleles labeled with Cy3, unmethylated labeled with Cy5
|
| |
|
| Hybridization protocol |
Hybridization was carried out according to Illumina directions by the Illumina Cspro service center at Oxford University.
|
| Scan protocol |
Scanning was carried out according to Illumina directions by the Illumina Cspro service center at Oxford University.
|
| Description |
For each normal/tumor pair, the sample numbers are paired but offset by one with the tumor being the lower of the two numbers. For example, 85040001 is the adenocarcinoma tumor profile that pairs with 85040002.
|
| Data processing |
Data processing was performed according to Illumina directions by the Illumina Cspro service center at Oxford University. Data were normalized using the average setting. Software was BSGX version 3.2.3.
Beta values (Intensity Ratio Values) represent methylation level of the CpG locus. ß-values were calculated using the ratio of intensities between methylated and unmethylated alleles, i.e., (Intensity of methylated bead type)/(Intensity of methylated bead type + Intensity of unmethylated bead type).
|
| |
|
| Submission date |
Nov 16, 2009 |
| Last update date |
Feb 25, 2014 |
| Contact name |
Ian Michael Wilson |
| E-mail(s) |
iwilson@bccrc.ca
|
| Phone |
6046758000x7703
|
| URL |
http://www.bccrc.ca/cg/people_iwilson.html
|
| Organization name |
British Columbia Cancer Research Centre
|
| Department |
Cancer Genetics
|
| Lab |
Wan Lam Lab
|
| Street address |
675 West 10th Avenue
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V5Z1L3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL8490 |
| Series (1) |
| GSE19034 |
EYA4 is a non-small cell lung cancer tumor suppressor located in the susceptibility locus on chromosome 6q |
|
