NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM333729 Query DataSets for GSM333729
Status Public on Jun 23, 2009
Title Patient 060 with adenocarcinoma
Sample type RNA
 
Channel 1
Source name Primary lung tumor
Organism Homo sapiens
Characteristics Annotation: AD060
Cohort: dataset I
Age: 56
Sex: M
Histology: AD
Smoking (BI): 1260
TNM (Pathological): T2N0M0
Stage (Pathological ): IB
Status: Dead
Survival (days): 440
Evidence of relapse: Y
Site of relapse: LN (neck)
EGFR status: Wt
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 0.1097 1.079
A_23_P100011 -4.2433 0.0528
A_23_P100022 -5.0209 0.0308
A_23_P100056 -1.2481 0.421
A_23_P100074 -0.5713 0.673
A_23_P100092 0.4457 1.362
A_23_P100103 0.0058 1.004
A_23_P100111 -0.7588 0.591
A_23_P100127 -0.7760 0.584
A_23_P100133 0.5470 1.461
A_23_P100141 -1.1234 0.459
A_23_P100156 -0.3789 0.769
A_23_P100177 3.2065 9.231
A_23_P100189 -0.6967 0.617
A_23_P100196 -0.3884 0.764
A_23_P100203 -0.0043 0.997
A_23_P100220 3.7474 13.43
A_23_P100240 -2.8573 0.138
A_23_P10025 1.8111 3.509
A_23_P100263 -0.8365 0.56

Total number of rows: 41000

Table truncated, full table size 1025 Kbytes.




Supplementary file Size Download File type/resource
GSM333729.txt.gz 14.2 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap