This dataset contains transcription profiles of TOP10 E.coli transformed with 85 rewired network plasmids first described in: Evolvability and hierarchy in rewired bacterial gene networks. Nature 452:840-5 (2008). The data are described and analysed in an accompanying paper Baumstark et al.,The propagation of perturbations in shuffled bacterial gene networks (Submitted, 2015). 260 raw data microarrays are provided in total, representing biological triplicates (a,b and c; independent colonies grown from the same transformation, under standard growth conditions; LB, 16h). This is done for each of 255 promoter-ORF constructs (e.g. appY-crp, etc.) and 5 control construct microarrays (empty plasmid; Co). Co controls are provided for comparison, to show the relative effect of the rewiring genetic perturbation. The final processed data compares the number of perturbed genes, comparing between the average expression values of each rewired construct and Co. Methods: The 85 rewiring plasmids (Isalan et al, 2008) were transformed into E. coli TOP10 cells and grown under standardised conditions: bacteria were freshly plated onto LB Agar plates (with 100 μg/ml Ampicillin and 50 μg/ml Streptomycin) and incubated overnight at 37oC to form colonies. Single colonies (<3 days old) were used to inoculate 2 ml of LB in 14 ml culture tubes, containing 100 μg/ml Ampicillin and 50 μg/ml Streptomycin. Constructs were grown for 16h at 37oC, at 220 rpm in an orbital shaker. 10 μg of extracted total bacterial RNA (integrity number > 7.0) was used with Affymetrix GeneChip E. coli Genome 2.0 Arrays. Key to names: RAW DATA samples 1-260 _Co_1a.CEL = Control Co, colony a _Co_1b.CEL = Control Co, colony b etc. appY_O_30a.CEL = appY-promoter only, colony a appY_O_30b.CEL = appY-promoter only, colony b etc. appY_crp_34a.CEL = rewired construct, appY-promoter expressing crp ORF, colony a appY_crp_34b.CEL = rewired construct, appY-promoter expressing crp ORF, colony b appY_crp_34b.CEL = rewired construct, appY-promoter expressing crp ORF, colony c etc. PROCESSED DATA sample 261: probe_set_expression_value_norm_all - normalised data for all samples, for all E. coli K12 genes sample 262: probe_set_expression_value_norm_MG1655 - normalised data for all samples, for E. coli MG1655 subset of genes
The propagation of perturbations in shuffled bacterial gene networks
None
No sample metadata fields
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Diagnosis of Kawasaki Disease Using a Minimal Whole-Blood Gene Expression Signature.
Sex
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Diagnostic Test Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile Children.
Sex, Specimen part, Disease, Disease stage
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Diagnosis of childhood tuberculosis and host RNA expression in Africa.
Disease
View SamplesGenome-wide analysis of transcriptional profiles in children <17 years of age with inflammatory diseases, bacterial or viral infections or with clinical features suggestive of infection.
Diagnosis of Kawasaki Disease Using a Minimal Whole-Blood Gene Expression Signature.
Sex
View SamplesTranscriptional profiles are increasingly used to investigate the severity, subtype and pathogenesis of disease. We now describe whole blood RNA signatures and local and systemic immune mediator levels in a large cohort of adults hospitalised with influenza from which extensive clinical and investigational data was obtained. Signatures reflecting interferon-related antiviral pathways were common up to day 4 of symptoms in cases not requiring mechanical ventilatory support; in those needing mechanical ventilation, an inflammatory, activated neutrophil and cell stress/death (bacterial) pattern was seen, even early after disease onset. Identifiable bacterial co-infection was not necessary for this bacterial signature but could enhance its development while attenuating the early viral signature. Our findings emphasise the importance of timing and severity in the interpretation of transcriptomic profiles and soluble mediator levels, and identify specific patterns of immune activation that may enable the development of novel diagnostics and therapeutics
Progression of whole-blood transcriptional signatures from interferon-induced to neutrophil-associated patterns in severe influenza.
Sex, Age, Race, Subject, Time
View SamplesThe study aimed to define transcriptional signatures for detection of active TB (TB) compared to latent TB infection (LTBI) as well as to other diseases (OD) with similar clinical phenotypes in patients with and without HIV in two African paediatric populations.
Diagnosis of childhood tuberculosis and host RNA expression in Africa.
Disease
View SamplesGenome-wide analysis of transcriptional profiles in children <17 years of age with bacterial or viral infections or with clinical features suggestive of infection.
Diagnostic Test Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile Children.
Sex, Specimen part
View SamplesGenome-wide analysis of transcriptional profiles in children <17 years of age with inflammatory diseases, bacterial or viral infections or with clinical features suggestive of infection.
Diagnosis of Kawasaki Disease Using a Minimal Whole-Blood Gene Expression Signature.
Sex
View SamplesThis SuperSeries is composed of the SubSeries listed below.
No associated publication
Sex, Age, Specimen part, Disease
View Samples