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Pseudomonas aeruginosa
9 Downloadable Samples
Illumina HiSeq 2500
Description
Extremely slow growth imposed by energy limitation is a ubiquitous but poorly understood physiological state for microbes. We used oxygen limitation to impose this state on Pseudomonas aeruginosa and measured newly synthesized proteins using a time-selective proteome labeling method (BONCAT) to identify relevant regulators and metabolic pathways. We further characterized one upregulated protein that has no homology to any known protein domains. This small, acidic protein is post-transcriptionally regulated and physically interacts with RNA polymerase, binding near the secondary channel during transcription elongation, and leading to widespread effects on gene expression. For some genes, the impacts on transcript and protein levels are different, suggesting possible modulation of translation as well. These effects have phenotypic consequences, as deletion of the gene affects biofilm formation, secondary metabolite production, and fitness in fluctuating conditions. Based on these phenotypes, we have designated the protein SutA (survival under transitions). Overall design: Profiles of rRNA-depleted total RNA from WT, ?sutA (PA14_69770), and SutA-overexpressing cells grown late exponential phase in minimal medium containing pyruate as the carbon source, in triplicate
Publication Title
SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
Objective: Dyslipidemia is one of the key factors behind coronary heart disease. Blood and lymphatic vessels play pivotal roles in both lipoprotein metabolism and development of atherosclerotic plaques. Recent studies have linked members of Vascular Endothelial Growth Factor (VEGF) family to lipid metabolism but the function of VEGF-D has remained unexplored. Here we investigated how the deletion of VEGF-D affects lipid and lipoprotein metabolism in atherogenic LDLR-/-ApoB100/100 mice. Approach and Results: Deletion of VEGF-D (Vegfd-/-LDLR-/-ApoB100/100) led to markedly elevated plasma cholesterol and triglyceride levels without an increase in atherogenesis. Size distribution and hepatic lipid uptake studies confirmed a delayed clearance of large chylomicron remnant particles that cannot easily penetrate through the vascular endothelium. Mechanistically, the inhibition of VEGF-D signaling significantly decreased the hepatic expression of syndecan 1 (SDC1), which is one of the main receptors for chylomicron remnant uptake when LDLR is absent. Immunohistochemical staining confirmed reduced expression of SDC1 in the sinusoidal surface of hepatocytes in VEGF-D deficient mice. Furthermore, hepatic RNA sequencing revealed that VEGF-D is also an important regulator of genes related to lipid metabolism and inflammation. The lack of VEGF-D signaling via VEGF receptor 3 led to lowered expression of genes regulating triglyceride and cholesterol production as well as downregulation of peroxisomal ß-oxidation pathway. Conclusions: These results demonstrate that VEGF-D, a powerful lymphangiogenic and angiogenic growth factor, is also a major regulator of chylomicron metabolism in mice. Overall design: Gene expression profiling of mouse liver tissue from control and VEGF-D knock-out mice. Control and VEGF-D KO mice were both in C57Bl/6 and atherosclerotic background, i.e., deficient of LDLR and expressing only apolipoprotein B100.
Publication Title
Deletion of Lymphangiogenic and Angiogenic Growth Factor VEGF-D Leads to Severe Hyperlipidemia and Delayed Clearance of Chylomicron Remnants.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 39 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
The cellular origin of Ewing tumor (ET), a tumor of bone or soft tissues characterized by specific fusions between EWS and ETS genes, is highly debated. Through gene expression analysis comparing ETs with a variety of normal tissues, we show that the profiles of different EWS-FLI1-silenced Ewing cell lines converge toward that of mesenchymal stem cells (MSC). Moreover, upon EWS-FLI1 silencing, two different Ewing cell lines can differentiate along the adipogenic lineage when incubated in appropriate differentiation cocktails. In addition, Ewing cells can also differentiate along the osteogenic lineage upon long-term inhibition of EWS-FLI1. These in silico and experimental data strongly suggest that the inhibition of EWS-FLI1 may allow Ewing cells to recover the phenotype of their MSC progenitor.
Publication Title
Mesenchymal stem cell features of Ewing tumors.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 21 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
To understand the contribution of the poly(A)binding protein to the translation of specific mRNAs, we compared the ribosome occupancy of mRNAs in wild type Arabidopsis and pab2 pab8 double mutant seedlings. The mutants continue to express the PAB4 paralog of PABP.
Publication Title
The global translation profile in a ribosomal protein mutant resembles that of an eIF3 mutant.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 17 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
To understand the contribution of the RPL24B protein, a component of the large 60S ribosomal subunit, to the translation of specific mRNAs, we compared the ribosome occupancy of mRNAs in wild type Arabidopsis and the rpl24b/stv1-1 T-DNA insertion mutant.
Publication Title
The global translation profile in a ribosomal protein mutant resembles that of an eIF3 mutant.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
The global translation profile in a ribosomal protein mutant resembles that of an eIF3 mutant.
Sample Metadata Fields
Age, Specimen part
View Samples
GSE28223- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
To understand the contribution of the k subunit of eukaryotic transcription factor 3 (eif3k) to the translation of specific mRNAs, we compared the polysome loading states and overall transcript levels of wild type Arabidopsis and the eif3k T-DNA insertion mutant by Affymetrix arrays.
Publication Title
The global translation profile in a ribosomal protein mutant resembles that of an eIF3 mutant.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Mitochondrial biogenesis is under the control of two different genetic systems: the nuclear genome (nDNA) and the mitochondrial genome (mtDNA). mtDNA is a circular genome of 16.6 kb encoding 13 of the approximately 90 subunits that form the respiratory chain, the remaining ones being encoded by the nuclear genome (nDNA). Eukaryotic cells are able to monitor and respond to changes in mitochondrial function through alterations in nuclear gene expression, a phenomenon first defined in yeast and known as retrograde regulation. With this experiment we aimed to identify the set of nuclear genes that significantly change their expression level in response to depletion of mtDNA.
Publication Title
How do human cells react to the absence of mitochondrial DNA?
Sample Metadata Fields
Cell line
View Samples GSE28222- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
To understand the contribution of the k subunit of eukaryotic transcription factor 3 (eif3k) to the translation of specific mRNAs, we compared the polysome loading states and overall transcript levels of wild type Arabidopsis and the eif3k T-DNA insertion mutant by Affymetrix arrays.
Publication Title
The global translation profile in a ribosomal protein mutant resembles that of an eIF3 mutant.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
A transcriptome analysis identifies molecular effectors of unconjugated bilirubin in human neuroblastoma SH-SY5Y cells.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples