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Title: Transcription profiling by array of human DU145 cells treated with small molecule MS0019266      
dateReleased:
10-01-2012
description:
This study is about high content screening small molecule compound as radiosensitizer. Two compounds were got finally from a chemical bank. Our data indicate cancer cell lines became more sensitive to radiation after treatment with both two compounds respectively. In order to know the mechanism, microarray was performed to try to find the target genes of one compound. DU145 cells were treated with MS0019266 (5 umol/L) for 8 hours and total RNA was extracted from treated and untreated cells respectively. Synthesis of cDNA from total RNA and hybridization/scanning of microarrays were performed with Affymetrix GeneST1.0 array as described in the GeneChip manual. The raw intensity data were extracted from the GeneChip using Gene Expression Console ( Affymetrix Inc.) and normalized across the chips by log scale robust multi-array analysis (RMA) method and the quality control of each chip data was performed by investigating overall intensity values for all probes, negative and positive controls. To identify significantly differentially expressed genes between groups such as treated vs. control samples, Significance Analysis of Microarray (SAM, version2.1) was carried out. SAM is a widely-used microarray differential analysis tool that correlates gene expression data to a wide variety of clinical parameters and uses permutation to estimate False Discovery Rate for multiple testing. The cutoff of FDR q value for SAM test was set to 0.1. The gene expression data was also integrated with Gene Ontology functional database using DAVID to perform functional enrichment for better interpretation of gene expression profiles in the context of biological functions.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-MTAB-845
refinement:
raw
keywords:
functional genomics
dateModified:
01-25-2012
creators:
Shibo Fu
availability:
available
types:
gene expression
name:
Homo sapiens
name:
compound treatement
ID:
A-AFFY-141
name:
Affymetrix GeneChip Human Gene 1.0 ST Array [HuGene-1_0-st-v1]
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-845/E-MTAB-845.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-MTAB-845/E-MTAB-845.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
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

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