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Title: Gene signature predictive of response to chemotherapy in mCRC [RT-PCR]      
dateReleased:
11-20-2013
description:
The objective is to generate a robust and validated predictor profile for chemotherapy response in patients with mCRC using microarray gene expression profiles of primary colorectal cancer tissue. To define a gene signature of response to chemotherapy in metastatic colorectal cancer, samples were obtained from 40 patients from Marques de Valdecilla Hospital who underwent primary surgery. Gene expression was detected and quantified using the Human Whole Genome U133 Plus 2.0 array (Affymetrix), containing 54675 human gene probes. The validation set consisted of 119 samples from Hospital Virgen del Rocio, Seville, Spain; Hospital Virgen de la Victoria, Malaga, Spain; Hospital de la Merced, Osuna, Spain and Hospital Marqués de Valdecilla, Santander, Spain, and included 86 tumor samples (40 coming from the training set and 46 from newly treated CRC patients) and 33 normal tissue samples of CRC patients used as controls. Custom-designed TaqMan® Low Density Arrays (TLDA) 7900 HT Micro Fluidic Cards including the 161 genes selected for validation were run and analyzed by the ABI PRISM® 7900HT Sequence Detection System (SDS 2.2, Applied Biosystems) according to manufacturer's protocol (Applied Biosystems). Expression of target miRNAs was normalized in relation to the expression of GAPDH. Cycle threshold (Ct) values were calculated using the SDS software v.4.2 using automatic baseline settings and a threshold of 0.2. Relative quantification of gene expression was calculated by the 2−ΔCt method (Applied Biosystems user bulletin no. 2 (P/N 4303859)). This submission represents the RT-PCR component of the study only
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-52513
refinement:
raw
alternateIdentifiers:
52513
keywords:
functional genomics
dateModified:
06-11-2014
availability:
available
types:
gene expression
name:
Homo sapiens
ID:
A-GEOD-17954
name:
Custom-designed TaqMan Low Density Arrays (TLDA) 7900 HT Micro Fluidic Cards
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-52513/E-GEOD-52513.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-52513/E-GEOD-52513.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52513
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress