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SRP119265
Mus musculus
2 Downloadable Samples
NextSeq 500
Description
Cell communication within tissues is mediated by multiple paracrine signals including growth factors, which control cell survival and proliferation. Cells and the growth factors they produce and receive constitute a circuit, yet the design features of cell circuits involved in tissue homeostasis are unknown. Here we used computational and experimental approaches to characterize the features of cell circuits based on growth factor exchange between macrophages and fibroblasts, two cell types found in most mammalian tissues. We found that the macrophage-fibroblast cell circuit is stable and robust to perturbations. We employed analytical screening of all possible two-cell circuit topologies and defined the circuit features sufficient for stability, including environmental constraint and negative feedback regulation. Moreover, we discovered that cell-cell contact was essential for the stability of the macrophage-fibroblast circuit. These findings highlight general principles of cell circuit design, and provide a new perspective on quantitative understanding of tissue homeostasis. Overall design: 1 sample of murine embryonic fibroblast and 1 sample murine bone marrow derived macrophages are analyzed for their expression of growth factors and growth factor receptors
Publication Title
Circuit Design Features of a Stable Two-Cell System.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Arabidopsis thaliana
- 16 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Low oxygen stress dynamically regulates the translation of cellular mRNAs as a means of energy conservation in seedlings of Arabidopsis thaliana. Most of the highly hypoxia-induced mRNAs are recruited to polysomes and actively translated, whereas other cellular mRNAs become translationally inactive and are either targeted for stabilization or degradation. Here we identify the involvement of OLIGOURIDYLATE BINDING PROTEIN 1 (UBP1), a triple RNA Recognition Motif protein, in dynamic and reversible aggregation of translationally repressed mRNAs during hypoxia. Mutation or downregulation of UBP1C interferes with seedling establishment and reduces survival of low oxygen stress. By use of messenger ribonucleoprotein immunopurification, we show that UBP1C constitutively binds a subpopulation of mRNAs characterized by U-rich 3-untranslated regions under normoxic conditions. During hypoxia, UBP1C association with non-U-rich mRNAs is enhanced concomitant with its aggregation into microscopically visible cytoplasmic foci, referred to as UBP1 stress granules (SGs). This UBP1C-mRNA association occurs as global levels of protein synthesis decline. Upon reoxygenation, rapid UBP1 SG disaggregation coincides with the return of the stabilized mRNAs to polysomes. The mRNAs that are highly induced and translated during hypoxia largely circumvent UBP1C sequestration. Thus, UBP1 is established as a component of dynamically assembled cytoplasmic mRNPs that sequester mRNAs that are poorly translated during a transient low energy stress.
Publication Title
Selective mRNA sequestration by OLIGOURIDYLATE-BINDING PROTEIN 1 contributes to translational control during hypoxia in Arabidopsis.
Sample Metadata Fields
Specimen part, Disease, Treatment
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Microarray experiment with polysomal and non-polysomal RNAs extracted under non-stress and mild-dehydration stress.
Publication Title
mRNA sequence features that contribute to translational regulation in Arabidopsis.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 38 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Transcriptome, translatome, and CSP1 RNA regulon analysis of 25-d-o Arabidopsis rosettes exposed to 12h low temperature (4C) treatment.
Publication Title
Cold shock protein 1 chaperones mRNAs during translation in Arabidopsis thaliana.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Cockayne syndrome (CS) is an inherited neurodevelopmental disorder with progeroid features. Although the genes responsible for CS have been implicated in a variety of DNA repair- and transcription-related pathways, the nature of the molecular defect in CS remains mysterious. We sought to define this defect by expression analysis of cells lacking functional CSB, a SWI/SNF-like ATPase that is responsible for most CS cases.
Publication Title
Cockayne syndrome group B protein (CSB) plays a general role in chromatin maintenance and remodeling.
Sample Metadata Fields
Subject
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
7d-old WT ler seedlings were submitted to 12h of non-stress (air) or hypoxia-stress treatment under low light conditions (45 uM m-2 s-2), and Total and Large Polysome RNA from both treatments were extracted and hybridized against Affymetrix genome chips. Values were used to evaluate changes in transcript abundance and transcript association with large polysomal complexes.
Publication Title
Genome-wide analysis of transcript abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 30 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Gene expression analysis of 7d-old Arabidopsis seedlings exposed to short term (2 h) hypoxia, long term (9 h) hypoxia, and 1 h reoxygenation after long term (9 h) hypoxia to evaluate the regulation of gene expression at the level of translation.
Publication Title
Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana.
Sample Metadata Fields
Age
View Samples- Arabidopsis thaliana
- 25 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
MPK6 shows transient increase in activity under hypoxia with maximal activity at 2 hrs. To study the role of MPK6 in hypoxia in Arabidopsis, 10 do seedlings of WT, mpk6 and MPK6 plants were exposed to 2 hrs hypoxia and 2hr air (mock).
Publication Title
Transient MPK6 activation in response to oxygen deprivation and reoxygenation is mediated by mitochondria and aids seedling survival in Arabidopsis.
Sample Metadata Fields
Specimen part
View Samples- Drosophila melanogaster
- 8 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Background The evolution of female choice mechanisms favouring males of their own kind is considered as crucial step during the early stages of speciation. However, although the genomics of mate choice may influence both the likelihood and speed of speciation, the identity and location of genes underlying assortative mating remain largely unknown.
Publication Title
Female Drosophila melanogaster gene expression and mate choice: the X chromosome harbours candidate genes underlying sexual isolation.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Saccharomyces cerevisiae
- 6 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Reactive oxygen species, generated in vivo or exogenously encountered, constantly challenge living organisms. Oxidation of polyunsaturated fatty acids (PUFA), which are susceptible to oxidant attack, can lead to initiation of lipid peroxidation and in turn rapid production of toxic lipid hydroperoxides. Eukaryotic microorganisms such as Saccharomyces cerevisiae can survive harsh industrial conditions that contain high levels of the PUFA linoleic acid and its oxidised derivative, linoleic acid hydroperoxide (LoaOOH). The precise signalling and response mechanisms induced by yeast to overcome lipid hydroperoxide stress are ill understood.
Publication Title
Transcriptomic insights into the molecular response of Saccharomyces cerevisiae to linoleic acid hydroperoxide.
Sample Metadata Fields
No sample metadata fields
View Samples