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Sample GSM333759 Query DataSets for GSM333759
Status Public on Jun 23, 2009
Title Patient 090 with adenocarcinoma
Sample type RNA
 
Channel 1
Source name Primary lung tumor
Organism Homo sapiens
Characteristics Annotation: AD090
Cohort: dataset I
Age: 74
Sex: M
Histology: AD
Smoking (BI): 800
TNM (Pathological): T1N0M0
Stage (Pathological ): IA
Status: Dead
Survival (days): 477
Evidence of relapse: Y
Site of relapse: Local rec.
EGFR status: Wt
K-ras Status: Wt
p53 Status: Wt
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

Data table header descriptions
ID_REF
VALUE log2 of PRE_VALUE: Normalized ratio (Cy5/Cy3) representing sample/reference
PRE_VALUE Normalized ratio (Cy5/Cy3) representing sample/reference

Data table
ID_REF VALUE PRE_VALUE
A_23_P100001 -0.3940 0.761
A_23_P100011 -2.3808 0.192
A_23_P100022 -3.7959 0.072
A_23_P100056 -3.0000 0.125
A_23_P100074 -0.1584 0.896
A_23_P100092 0.0607 1.043
A_23_P100103 -1.4860 0.357
A_23_P100111 0.1097 1.079
A_23_P100127 -1.6038 0.329
A_23_P100133 0.0144 1.01
A_23_P100141 -0.8262 0.564
A_23_P100156 -0.9462 0.519
A_23_P100177 0.9351 1.912
A_23_P100189 -1.5146 0.35
A_23_P100196 -1.0321 0.489
A_23_P100203 0.1686 1.124
A_23_P100220 0.7706 1.706
A_23_P100240 -3.0116 0.124
A_23_P10025 -2.2934 0.204
A_23_P100263 -0.4941 0.71

Total number of rows: 41000

Table truncated, full table size 1029 Kbytes.




Supplementary file Size Download File type/resource
GSM333759.txt.gz 14.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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