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Sample GSM333770 Query DataSets for GSM333770
Status Public on Jun 23, 2009
Title Patient 111 with adenocarcinoma
Sample type RNA
 
Channel 1
Source name Primary lung tumor
Organism Homo sapiens
Characteristics Annotation: AD111
Cohort: dataset II
Age: 63
Sex: M
Histology: AD
Smoking (BI): 2350
TNM (Pathological): T2N0M0
Stage (Pathological ): IB
Status: Alive
Survival (days): 1955
Evidence of relapse: Y
Site of relapse:
EGFR status: Wt
K-ras Status: Mut
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 II
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 -0.8678 0.548
A_23_P100011 -1.9159 0.265
A_23_P100022 -4.0954 0.0585
A_23_P100056 -3.3823 0.0959
A_23_P100074 0.2774 1.212
A_23_P100092 0.6452 1.564
A_23_P100103 -0.2413 0.846
A_23_P100111 -0.9024 0.535
A_23_P100127 -1.9546 0.258
A_23_P100133 -1.5146 0.35
A_23_P100141 -0.4800 0.717
A_23_P100156 -0.3846 0.766
A_23_P100177 -0.2951 0.815
A_23_P100189 -0.1172 0.922
A_23_P100196 -2.0000 0.25
A_23_P100203 -1.3437 0.394
A_23_P100220 2.1276 4.37
A_23_P100240 4.2570 19.12
A_23_P10025 -1.7612 0.295
A_23_P100263 -0.6597 0.633

Total number of rows: 41000

Table truncated, full table size 1024 Kbytes.




Supplementary file Size Download File type/resource
GSM333770.txt.gz 14.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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