|
| Status |
Public on Jun 23, 2009 |
| Title |
Patient 005 with adenocarcinoma |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Primary lung tumor
|
| Organism |
Homo sapiens |
| Characteristics |
Annotation: AD005
Cohort: dataset I
Age: 67
Sex: F
Histology: AD
Smoking (BI): 0
TNM (Pathological): T1N2M0
Stage (Pathological ): IIIA
Status: Dead
Survival (days): 1200
Evidence of relapse: Y
Site of relapse: PM
EGFR status: Mut
K-ras Status: Wt
p53 Status: Mut
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 500 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.
|
| Label |
Cy5
|
| Label protocol |
cRNA was generated and labeled with Cy3 or Cy5 (CyDye, Amersham Pharmacia Biotech, Piscataway, NJ) using the Low RNA Fluorescen
|
| |
|
| Channel 2 |
| Source name |
Total RNA from 20 lung cell lines representing all major histological types of lung cancers, labeled with Cyanine-3 (green).
|
| Organism |
Homo sapiens |
| Characteristics |
n/a
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 500 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.
|
| Label |
Cy3
|
| Label protocol |
cRNA was generated and labeled with Cy3 or Cy5 (CyDye, Amersham Pharmacia Biotech, Piscataway, NJ) using the Low RNA Fluorescen
|
| |
|
| |
| Hybridization protocol |
standard Affymetrix protocol
|
| Scan protocol |
Whole Human Genome oligo DNA microarray with 41000 distinct probes was scanned using an Agilent DNA microarray scanner (G2505B, Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version 9.5).
|
| Description |
dataset I
|
| Data processing |
LOWESS normalized, background subtracted VALUE data obtained from ratio of processed Red signal/processed Green signal using GeneSpring software.
|
| |
|
| Submission date |
Oct 15, 2008 |
| Last update date |
Jun 23, 2009 |
| Contact name |
Takashi Takahashi |
| Organization name |
Aichi Cancer Center
|
| Street address |
1-1 Kanokoden, Chikusa-ku
|
| City |
Nagoya |
| State/province |
Aichi |
| ZIP/Postal code |
464-8681 |
| Country |
Japan |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE13213 |
Relapse-related molecular signature in lung adenocarcinomas identifies patients with dismal prognosis |
|
