|
| Status |
Public on Apr 30, 2015 |
| Title |
lung, adenocarcinoma_19840 |
| Sample type |
genomic |
| |
|
| Source name |
lung, adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: lung
patient_id1: 19840T
patient_id: 19840
analysis batch: 1
Sex: Male
race: European American
age: 79
disease state: non-small cell lung cancer (NSCLC)
histology: adenocarcinoma
7th tnm stage: Ib
tumor size (cm): 4
smoking status: ever
smoking packyears: 4
kras status: WT
tp53 mutation: unknown
death due to cancer: no
survival after surgery (days): 995
|
| 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 Beta 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) |
|
