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Sample GSM780629 Query DataSets for GSM780629
Status Public on Oct 25, 2012
Title LM444
Sample type RNA
 
Source name BATTLE_trial_core biopsy_chemorefractory non-small cell lung cancer
Organism Homo sapiens
Characteristics egfr mutation: WT
kras mutation: WT
egfr index: -0.02
histology-iw revised: Squamous Cell Carcinoma
egfr-iw type: No
kras-iw mutation (yes/no): No
gender: Female
race: White
stage_at_diagnosis: IB
prior_tx_for_mets: 0
smoking_status: Former
biopsy site (grouped): 5: Adrenal
treatment: sorafenib
markergroup: 3
8-week disease control (1=yes, 0=no): 0
randomization_date: 2009-04-29
date_of_progression: 1-Jun-09
pfsc (1=progressed; 0=not progressed): 1
pfsm (month): 1.0842
Treatment protocol Samples were OCT-embedded and frozen before RNA extraction
Growth protocol Core biopsies from patients included in the Biomarker-integrated Approaches of Targeted Therapy for Lung Cancer Elimination (BATTLE)
Extracted molecule total RNA
Extraction protocol RNA was extracted and purified from OCT-embedded tissue using the RNeasy Mini Kit (Qiagen) including on-column DNase (Qiagen) digestion as described by the manufacturer's protocol.
Label biotin
Label protocol RNA amplifications were performed using the WT-Amplification™ Pico (NuGEN) kit. WT-Ovation™ Pico products (NuGEN) are labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). Each labeled cRNA targets are synthesized according to manufacturer's protocols. The quantity and quality of the amplified cRNA or cDNA were assessed by a ND-1000 spectrophotometer (Nanodrop Technologies), and Agilent Bioanalyzer (Agilent Technologies), respectively.
 
Hybridization protocol Hybridization mixtures were prepared according to Affymetrix procedures to accommodate 5 μg of cDNA targets from NuGEN amplification. Human Gene 1.ST platform were hybridized, revealed and washed according to the Affymetrix protocol.
Scan protocol Gene chips were scanned using a 7 G scanner (Affymetrix) and images (DAT files) were converted to CEL files using GCOS software (Affymetrix).
Description LM001_525_AGE_1_LM444_08_19_09
Inclusion number in the clinical trial : 278
Data processing Raw data of microarrays were processed using quantile normalization and RMA algorithm (RMAExpress); expression values were log2 transformed
 
Submission date Aug 16, 2011
Last update date Oct 25, 2012
Contact name Pierre Saintigny
E-mail(s) [email protected]
Organization name The University of Texas M.D. Anderson Cancer Center
Department Thoracic / Head and Neck Medical Oncology
Street address 1515 Holcombe
City Houston
ZIP/Postal code 77030
Country USA
 
Platform ID GPL6244
Series (3)
GSE31428 Final efficacy and biomarker analysis of the sorafenib arm of the BATTLE (Biomarker-Integrated Approaches of Targeted Therapy for Lung Cancer Elimination) trial
GSE31852 An EGFR-mutation signature reveals features of the EGFR-dependent phenotype and identifies MACC1 as an EGFR-associated regulator of MET.
GSE33072 An epithelial-mesenchymal transition (EMT) gene signature predicts resistance to erlotinib and PI3K pathway inhibitors and identifies Axl as a novel EMT marker in non-small cell lung cancer.

Data table header descriptions
ID_REF
VALUE log2-RMA signal

Data table
ID_REF VALUE
8023672 11.28
8128282 5.69
8063634 7.6
8177085 4.84
8142899 8.42
8155525 6.66
8130916 9.12
7924893 9.12
8122933 6.46
7981215 7.49
7991296 7.6
8103620 3.2
8163000 8.76
8083223 8.66
8024708 8.79
7953351 9.01
7982574 7.94
7976778 6.67
7988342 5.9
7896699 8.23

Total number of rows: 33297

Table truncated, full table size 422 Kbytes.




Supplementary file Size Download File type/resource
GSM780629_LM001_525_AGE_1_LM444_08_19_09.CEL.gz 4.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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