RNA-Seq of purified P-bodies from HEK293 cells
Ontology highlight
ABSTRACT:
INSTRUMENT(S): NextSeq 500
ORGANISM(S): Homo sapiens
SUBMITTER: Hubstenberger Arnaud
PROVIDER: E-MTAB-5477 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The homeodomain protein Meis1 is essential for definitive hematopoiesis and vascular patterning in the mouse embryo. Our present study suggested it exerts two distinguishable effects in differentiating ES cells. First, it increases the numbers of hematopoietic progenitors and extends their persistence in culture. Second, Meis1 skews hematopoietic differentiation by suppressing erythroid while enhancing megakaryocytic progenitor differentiation. To identify the underlying transcriptional bases of these actions, we carried out microarray analysis to compare the various populations of cells developing in ES differentiation cultures in the presence and absence of Meis1 induction. ES cells with dox-inducible Meis1 (A2lox.Meis1) were differentiated as embryoid bodies (EBs) for 6 days before plating on OP9-GFP cell monolayers and cytokines, and treated with (+) or without (-) doxycycline (dox). Cells were purified by cell sorting on day 7 or 8 into various populations based on levels of CD41 expression: GFP-CD41-, GFP-CD41+ (day 7) and GFP-CD41-,GFP-CD41int, and GFP-CD41hi (day 8). Gene expression of these purified populations was determined by microarray analysis.
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Project description:The homeodomain protein Meis1 is essential for definitive hematopoiesis and vascular patterning in the mouse embryo. Meis2, another member of the same family, shares 82% protein identities with Meis1. Our present study suggested Meis2 exerts two distinguishable effects in differentiating ES cells. First, it increases the numbers of hematopoietic progenitors and extends their persistence in culture. Second, Meis2 skews hematopoietic differentiation by suppressing erythroid while enhancing megakaryocytic progenitor differentiation. To identify the underlying transcriptional bases of these actions, we carried out microarray analysis to compare the various populations of cells developing in ES differentiation cultures in the presence and absence of Meis2 induction. ES cells with dox-inducible Meis2 (A2lox.Meis2) were differentiated as embryoid bodies (EBs) for 6 days before plating on OP9-GFP cell monolayers and cytokines, and treated with (+) or without (-) doxycycline (dox). Cells were purified by cell sorting on day 7 or 8 into various populations based on levels of CD41 expression: GFP-CD41-, GFP-CD41+ (day 7) and GFP-CD41-,GFP-CD41int, and GFP-CD41hi (day 8). Gene expression of these purified populations was determined by microarray analysis.
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Project description:To address the dynamics of RNA storage within context of the cell cycle, we set out to purify p-bodies from various cell cycle stages.This was done using Fluorescent Activated Particle Sorting (FAPS) on HEK293 cells synchronized at mid G1, G1S, mid S, or G2M phases. For every cell cycle phase, 2 fractions are sequenced: (i) the purified PB fraction, (ii) or the corresponding cytoplasm before purification. Each fraction in each cell cycle phase is done in 3 biological replicates (with the exception of 2 instances having 2 replicates) for a total of 28 samples.
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Project description:LC-MS/MS was conducted to characterize the proteome of P-bodies in HeLa cells.
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Project description:Calcium channel B subunits (CavB) are mainly recognized for their contribution as regulatory subunits in modulating biophysical and trafficking channel properties. Here, we report for a novel function of the neuronal auxiliary CavB4 subunit in nuclear localization and transcriptional activity. In CA1 hippocampal neurons, nuclear translocation of CavB4 is differentiation-dependent. Similarly, in NG108-15 cell line, the nuclear localization of CavB4 is triggered by cAMP, a neuronal differentiating factor. The nuclear translocation of CavB4 requires an intact SH3 / GK interaction and is lost for a 38 amino acid C-terminal truncated form of the subunit implicated in human juvenile myoclonic epilepsy (CavB4-R482X mutant). The nuclear localization of CavB4 induces the regulation of numerous of genes which is not the case for the human mutation. These data indicate that gene regulation by a calcium channel subunit may contribute to the acquisition of a neuronal phenotype, a process that is disturbed if the nuclear localization is hampered by a mutation implicated in a severe neurological phenotype.
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2012-08-02 | E-GEOD-34583 | biostudies-arrayexpress
Project description:We have been interested whether peripheral tolerance can be restored by vaccination with antigen-presenting cells (APCs) loaded with apoptotic bodies. Dendritic cells (DCs) are powerful APCs that have a critical role in the initiation and progression of autoimmunity. We previously demonstrated that DCs loaded with apoptotic islet cells prevents experimental type 1 diabetes (T1D), an autoimmune disease caused by beta-cell destruction. The goal of this study is to characterize the molecular changes on gene expression -transcriptome- occurring in these DCs pulsed with apoptotic bodies. Cells from four different genetically identical NOD (Non-Obese Diabetic) mice were used to obtain DCs. DCs were loaded with apoptotic bodies from NIT-1 cell line (insulinoma from NOD mice). Unloaded DCs were used as control in four paired experiments. Moreover, transcriptome from NIT-1 apoptotic bodies was determined. Mouse Gene 1.0 ST Arrays from Affymetrix (28,853 genes) were hybridized and genes with a p-value <= 0.002, adjusted p-value <= 0.08 and fold change (FC) >= 1.38 were considered upregulated, and genes with FC <= -1.37 were considered downregulated. Results demonstrate that apoptotic cells engulfment promotes molecular changes in DCs towards tolerogenic features. Gene expression profile of DCs from NOD mice that captured NIT-1 apoptotic bodies showed a downregulation of genes involved in antigen presentation and differential expression of cytokine, chemokine, natural immunity and immunoregulation genes together with the presence of specific transcripts for islet autoantigens. Molecular changes of DCs caused by the uptake of apoptotic bodies are key factors to induce antigen-specific peripheral tolerance.
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