|
| Status |
Public on Apr 30, 2015 |
| Title |
lung, adenocarcinoma_14468 |
| Sample type |
genomic |
| |
|
| Source name |
lung, adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: lung
patient_id1: 14468T
patient_id: 14468
analysis batch: 2
Sex: Male
race: African American
age: 51
disease state: non-small cell lung cancer (NSCLC)
histology: adenocarcinoma
7th tnm stage: Ib
tumor size (cm): 2
smoking status: ever
smoking packyears: 49
kras status: WT
tp53 mutation: WT
death due to cancer: no
survival after surgery (days): 3362
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was extracted and purified from tissue samples using Qiagen DNeasy Kit according to standard instructions
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
adenocarcinoma
|
| Data processing |
BeadStudio software v3.2; Fluorescent signals were collated via Bead Studio software and converted into -values. Illumina Bead Studio software output data were normalized using SSN (simple scaling normalization), to correct for dye bias and transformed into M-values (M = log2 intensity of methylated probe/ intensity of unmethylated probe), using the R package lumi. Raw signals can be found on the series level in the file Unmethylated_and_methylated_signal_intensities.txt
|
| |
|
| Submission date |
Nov 17, 2014 |
| Last update date |
Apr 30, 2015 |
| Contact name |
Ana I Robles |
| E-mail(s) |
Ana_Robles@nih.gov
|
| Phone |
301-496-1729
|
| Organization name |
National Cancer Institute/NIH
|
| Lab |
Laboratory of Human Carcinogenesis
|
| Street address |
37 Convent Dr 37/3060D
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL8490 |
| Series (1) |
| GSE63384 |
Multi-platform Characterization of Stage I Lung Adenocarcinoma (Genome-wide DNA Methylation) |
|
