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Series GSE58553 Query DataSets for GSE58553
Status Public on Jun 17, 2014
Title An Integrated Approach to Reconstructing Genome-scale Transcriptional Regulatory Networks [Affymetrix]
Platform organism Cereibacter sphaeroides 2.4.1
Sample organism Cereibacter sphaeroides
Experiment type Expression profiling by array
Summary Rhodobacter sphaeroides is the best studied photosynthetic bacterium, yet much remains unknown about its transcriptional regulatory processes on a genome-scale. We developed a work-flow for genome-scale reconstruction of transcriptional regulatory networks and applied it to sequence and gene expression data sets available for R. sphaeroides. To assess the predictive performance of our reconstructed model, we generated global transcript level and/or protein-DNA interaction data for 3 transcription factors (PpsR, RSP_0489 and RSP_3341). This dataset contains global transcript level analyses for RSP_0489 and RSP_3341 deletion strains, as well as matching wild type controls.
 
Overall design Microarray analysis conducted for deletion strains of 2 previously uncharacterized transcription factors predicted to be involved in the regulation of carbon metabolism and iron homeostasis in R. sphaeroides using the R. sphaeroides Affymetrix gene chip. These deletion mutant expression profiles were compared to that of wild type cells to determine differentially expressed genes regulated by these transcription factors.
 
Contributor(s) Imam S, Donohue TJ
Citation(s) 25723545
Submission date Jun 16, 2014
Last update date Apr 13, 2015
Contact name Timothy J Donohue
E-mail(s) tdonohue@bact.wisc.edu
Phone 608-265-8465
Organization name University of Wisconsin - Madison
Department Bacteriology
Lab Timothy Donohue
Street address 1552 University Avenue
City Madison
State/province WI
ZIP/Postal code 53726
Country USA
 
Platforms (1)
GPL162 [uwyRhodo1a] Rhodobacter sphaeroides 2.4.1 GeneChip
Samples (11)
GSM1413829 RSP_3341_Rep1
GSM1413830 RSP_3341_Rep2
GSM1413831 WT_Photo_Rep1
This SubSeries is part of SuperSeries:
GSE58658 An Integrated Approach to Reconstructing Genome-scale Transcriptional Regulatory Networks
Relations
BioProject PRJNA252860

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
GSE58553_Normalized_data_Affy_ProbeSet_Name.txt.gz 280.6 Kb (ftp)(http) TXT
GSE58553_RAW.tar 9.8 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
Processed data are available on Series record

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