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Sample GSM333746 Query DataSets for GSM333746
Status Public on Jun 23, 2009
Title Patient 077 with adenocarcinoma
Sample type RNA
 
Channel 1
Source name Primary lung tumor
Organism Homo sapiens
Characteristics Annotation: AD077
Cohort: dataset I
Age: 60
Sex: F
Histology: AD
Smoking (BI): 0
TNM (Pathological): T1N0M0
Stage (Pathological ): IA
Status: Alive
Survival (days): 2348
Evidence of relapse: N
Site of relapse:
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

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 -0.9546 0.516
A_23_P100011 -2.6804 0.156
A_23_P100022 -2.9434 0.13
A_23_P100056 -4.0565 0.0601
A_23_P100074 -1.1078 0.464
A_23_P100092 -0.7226 0.606
A_23_P100103 -1.1329 0.456
A_23_P100111 -1.3474 0.393
A_23_P100127 -4.9794 0.0317
A_23_P100133 -0.4286 0.743
A_23_P100141 -0.8730 0.546
A_23_P100156 -0.4860 0.714
A_23_P100177 0.9848 1.979
A_23_P100189 0.3242 1.252
A_23_P100196 -1.3437 0.394
A_23_P100203 -0.3219 0.8
A_23_P100220 1.5568 2.942
A_23_P100240 -3.5014 0.0883
A_23_P10025 -1.9490 0.259
A_23_P100263 -1.0710 0.476

Total number of rows: 41000

Table truncated, full table size 1023 Kbytes.




Supplementary file Size Download File type/resource
GSM333746.txt.gz 14.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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