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Series GSE45838 Query DataSets for GSE45838
Status Public on Sep 01, 2013
Title Knock-down of BCL6 expression in human Diffuse Large B-Cell Lymphoma cell lines
Organism Homo sapiens
Experiment type Expression profiling by array
Summary This dataset was used to benchmark the Virtual Inference of Protein-activity by Regulon Readout algorithm (VIPER). Despite recent advances in molecular profiling, proteome-wide assessment of protein activity in individual samples remains a highly elusive target. In stark contrast, protein activity quantitation is increasingly critical to the dissection of key regulatory processes and to the elucidation of biologically relevant mechanisms. Importantly, its value extends to the study of drug activity, as most small molecules inhibit activity of their cognate protein substrates without affecting the protein’s or associated mRNA’s abundance.
VIPER leverages the increasingly accurate and context specific knowledge of regulatory networks. Specifically, it uses the expression of the transcriptional targets most directly regulated by a given protein in an individual sample as a reporter for the computational inference of its activity.
 
Overall design BCL6 knock down experiments were performed in OCI-Ly7 and Pfeiffer GCB-DLBCL cell lines. Both cell lines were maintained in 10% FBS supplemented IMDM medium and transiently transfected with either a BCL6-specific or a non-target control siRNA oligo in triplicate. Total RNA was isolated 48h after transfection and gene expression was profiled on H-GU133plus2 Affymetrix gene chips.
 
Contributor(s) Ye BH, Ding BB
Citation(s) 27322546
Submission date Apr 06, 2013
Last update date Mar 25, 2019
Contact name Mariano Javier Alvarez
E-mail(s) malvarez@c2b2.columbia.edu
Organization name Columbia University
Department Joint Centers for Systems Biology
Lab Systems Biology
Street address 1130 St. Nicholas ave.
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (12)
GSM1116380 OCI-Ly7 NTsiRNA 1
GSM1116381 OCI-Ly7 NTsiRNA 2
GSM1116382 OCI-Ly7 NTsiRNA 3
Relations
BioProject PRJNA196519

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
GSE45838_RAW.tar 60.1 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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