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Series GSE60408 Query DataSets for GSE60408
Status Public on Jul 08, 2015
Title Expression profiles in 3 different B-cell lymphoma cell lines treated by 92 FDA approved compounds
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Identifying the Mechanism of Action (MoA) of drugs is critical for the development of new drugs, understanding their side effects, and drug repositioning. However, identifying drug MoA has been challenging and has been traditionally attempted only though large experimental setups with little success. While advances in computational power offers the opportunity to achieve this in-silico, methods to exploit existing computational resources are still in their infancy. To overcome this, we developed a novel method to identify Drug Mechanism of Action using Network Dysregulation (DeMAND).
The method is based on the realization that drugs affect the protein activity of their targets, but not necessarily their mRNA expression levels. In contrast, the change in protein activity directly affects the mRNA expression levels of downstream genes. Based on this hypothesis, DeMAND identifies drug MoA by comparing gene expression profiles following drug perturbation with control samples, and computing the change in the individual interactions within a pre-determined integrated transcriptional and post-translational regulatory model (interactome).
 
Overall design This dataset includes GEPs in 3 different B-cell lymphoma cell lines (OCI-LY3, OCI-LY7 and U2932) at 6, 12, and 24hrs. 92 FDA approved compounds were used at a concentration of IC20 at 24h. DMSO was used as control at each time-point. A total of 828 samples and 29 control samples were available for analysis. Total RNA was isolated with the RNAqueous-96 Automated Kit (Ambion) on the Janus automated liquid handling system (Perkin Elmer Inc.), quantified by NanoDrop 6000 spectrophotometer and quality checked by Agilent Bioanalyzer. 300ng of each of the samples with RIN value >7 were converted to biotinylated cRNA with the Illumina TotalPrep-96 RNA Amplification Kit (Ambion) using a standard T7-based amplification protocol and hybridized on the Human Genome U219 96-Array Plate (Affymetrix). Hybridization, washing, staining and scanning of the array plates were performed on the GeneTitan Instrument (Affymetrix) according to manufacturer’s protocols.
 
Contributor(s) Woo JH, Shimoni Y, Bansal M, Mattioli M, Karan C, Califano A
Citation(s) 26186195
Submission date Aug 13, 2014
Last update date Mar 21, 2019
Contact name Andrea Califano
Organization name Columbia University
Street address 1130 St. Nicholas Avenue, Rm. 906
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platforms (1)
GPL13667 [HG-U219] Affymetrix Human Genome U219 Array
Samples (864)
GSM1478336 REF_HeLa_NA_TH001_NG_101118_03_A01
GSM1478337 SULCONAZOLE.NITRATE_OCI-Ly7_6_TH001_NG_101118_03_A02
GSM1478338 CLOMIPHENE.CITRATE_OCI-Ly7_6_TH001_NG_101118_03_A03
Relations
BioProject PRJNA258206

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE60408_RAW.tar 1.9 Gb (http)(custom) TAR (of CEL)
Processed data included within Sample table
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