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Series GSE49914 Query DataSets for GSE49914
Status Public on Mar 27, 2014
Title ChIP-on-chip of OmpR binding in Salmonella enterica serovar Typhimurium strain SL1344 and E.scherichia coli strain CSH50 at pH 7 and pH 4.5 including analysis of OmpR binding in SL1344 in the absence and presence of novobiocin (25 μg/ml)
Platform organisms Escherichia coli K-12; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Sample organisms Escherichia coli K-12; Salmonella enterica subsp. enterica serovar Typhimurium
Experiment type Genome binding/occupancy profiling by array
Summary OmpR is a DNA binding protein belonging to the OmpR/EnvZ two component system. This system is known to sense changes in osmolarity in Escherichia coli. Recently, OmpR in Salmonella enterica serovar Typhimurium was found to be activated by acidic pH and DNA relaxation. In this study, ChIP-on-chip was employed to ascertain the genome-wide distribution of OmpR in Salmonella Typhimurium and Escherichia coli in acidic and neutral pH. In addition we investigated the affect of DNA relaxation on OmpR binding in Salmonella Typhimurium.
 
Overall design Analysis of OmpR binding at pH 7 and pH 4.5 in E-minimal medium in both SL1344 and CSH50. Three independent biological replicates at each pH 7 and pH 4.5 was performed. This was done in each strain background. DNA was immunopreciptated using an anti-FLAG anitbody which binds to flag-tagged OmpR in both strains. Two control ‘mock’ experiments were performed under the same culture condtions in each strain background; DNA was immunopreciptated using normal mouse IgG antibody. To analyse the effect of DNA relaxation onOmpR binding SL1344 was maintained in the exponential growth phase in LB broth with and without treatment with the drug novobiocin (25 μg/ml) for 40 min. This was peformed on two independent occasions. In all cases the experimental immunoprecipitated DNA was hybridised against the input DNA.
 
Contributor(s) Quinn HJ, Cameron AD, Dorman CJ
Citation(s) 24603618
Submission date Aug 15, 2013
Last update date Mar 28, 2014
Contact name Heather J Quinn
E-mail(s) [email protected]
Organization name Trinity College Dublin
Department Microbiology
Street address College green
City Dublin
ZIP/Postal code 2
Country Ireland
 
Platforms (2)
GPL10008 Oxford Gene Technology Chip2 Salmonella typhimurium microarray SL1344 strain product code: 010021
GPL17580 Agilent-019492 Project-0160-002
Samples (21)
GSM1209621 SL1344 E-minimal medium pH 7 90 min replicate 1
GSM1209622 SL1344 E-minimal medium pH 7 90 min replicate 2
GSM1209623 SL1344 E-minimal medium pH 7 90 min replicate 3
Relations
BioProject PRJNA215321

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
GSE49914_RAW.tar 89.4 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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