NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM333716 Query DataSets for GSM333716
Status Public on Jun 23, 2009
Title Patient 047 with adenocarcinoma
Sample type RNA
 
Channel 1
Source name Primary lung tumor
Organism Homo sapiens
Characteristics Annotation: AD047
Cohort: dataset I
Age: 46
Sex: M
Histology: AD
Smoking (BI): 0
TNM (Pathological): T1N1M0
Stage (Pathological ): IIA
Status: Alive
Survival (days): 2729
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 0.3092 1.239
A_23_P100011 -1.4540 0.365
A_23_P100022 -3.1078 0.116
A_23_P100056 -3.7681 0.0734
A_23_P100074 -1.2311 0.426
A_23_P100092 -0.2636 0.833
A_23_P100103 0.1596 1.117
A_23_P100111 -0.3997 0.758
A_23_P100127 -3.7447 0.0746
A_23_P100133 -0.3808 0.768
A_23_P100141 -0.4055 0.755
A_23_P100156 -0.8186 0.567
A_23_P100177 1.9050 3.745
A_23_P100189 -0.8365 0.56
A_23_P100196 -1.4941 0.355
A_23_P100203 -0.5670 0.675
A_23_P100220 1.1250 2.181
A_23_P100240 -0.9856 0.505
A_23_P10025 -2.4982 0.177
A_23_P100263 0.2461 1.186

Total number of rows: 41000

Table truncated, full table size 1023 Kbytes.




Supplementary file Size Download File type/resource
GSM333716.txt.gz 14.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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