Dynamic profiling of the protein life cycle in response to pathogens
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE59793MSV000078994
PROVIDER: PRJNA256211 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1525500_1.fastq.gz | Fastqsanger.gz | |||
| SRR1525500_2.fastq.gz | Fastqsanger.gz | |||
| SRR1525510_1.fastq.gz | Fastqsanger.gz | |||
| SRR1525510_2.fastq.gz | Fastqsanger.gz | |||
| SRR1525520_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 54 |
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Project description:Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle.
2015-03-06 | GSE59792 | GEO
Project description:Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle. Mouse primary dendritic cells were treated with LPS or mock stimulus and profiled over a 12-hour time course. Cells were grown in M-labeled SILAC media, which was replaced with H-labeled SILAC media at time 0. Aliquots were taken at 0, 0.5, 1, 2, 3, 4, 5, 6, 9, and 12 hours post-stimulation and added to equal volumes of a master mix of unlabeled (L) cells for the purpose of normalization. RNA-Seq was performed at 0, 1, 2, 4, 6, 9, and 12 hours post-stimulation.
2015-03-06 | E-GEOD-59792 | biostudies-arrayexpress
Project description:Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle.
2015-03-06 | GSE59784 | GEO
Project description:Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle. Mouse primary dendritic cells were treated with LPS or mock stimulus and profiled over a 12-hour time course. Cells were grown in M-labeled SILAC media, which was replaced with H-labeled SILAC media at time 0. Aliquots were taken at 0, 0.5, 1, 2, 3, 4, 5, 6, 9, and 12 hours post-stimulation and added to equal volumes of a master mix of unlabeled (L) cells for the purpose of normalization. RNA-Seq was performed at 0, 1, 2, 4, 6, 9, and 12 hours post-stimulation.
2015-03-06 | E-GEOD-59784 | biostudies-arrayexpress
Project description:Jovanovic M,Rooney M, Mertins P, Przybylski D, Chevrier N, Satija R, Rodriguez EH, Fields AP, Schwartz S, Raychowdhury R, Mumbach M, Eisenhaure T, Rabani M, Gennert D, Lu D, Delorey T, Weissman JS, Carr SA, Hacohen N, Regev A, submitted 2015. Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle.
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Project description:This SuperSeries is composed of the SubSeries listed below.
2015-03-06 | GSE59793 | GEO
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2010-05-16 | E-GEOD-17026 | biostudies-arrayexpress
Project description:mRNA expression profiles of trypanosomes from two discrete bloodstream form stages of the parasite (slender and stumpy forms), as well as during the transition of the stumpy population to the procyclic life-cycle stage were studied. Our analysis represents the first comparison of in vivo derived pleomorphic slender cells with genetically identical stumpy forms, and a first analysis of the dynamic changes in mRNA profile that accompany the transition to procyclic forms.
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Project description:Dynamic profiling of the protein life cycle in response to pathogens (protein)
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Project description:RNA-binding proteins (RBPs) target RNA in a context-dependent manner to regulate gene expression. Protein-protein interaction (PPI) maps of RBP complexes and networks are critical for defining RBP function and RNA targeting. Yet, PPI networks under-represent RBP baits and need more information about RNA-driven interactions. Therefore, we generated an RNA-aware, RBP-interactome map combining two strategies that use systematic proteomic methods to identify 1) protein interactions using co-immunoprecipitation in the presence or absence of RNase treatment of a ~100 RBPs across the RNA life-cycle and 2) RNA-dependent complexes using Size Exclusion Chromatography. Together, this dataset provides proteome-wide, cell-type specific, and quantitative identification of RNA-protein interactions across multiple RNA processing events. In the resulting PPI network, several hundred database-supported interactions establish many complexes operating at each of these mRNA life-cycle stages. Nearly a thousand novel interactions imply new functions for RBPs across multiple steps of the RNA life cycle. Overlapping our network with eCLIP data, we find RNA targets between interactors and uncover complex-driven binding signatures. Betweenness-centrality scores identify multi-functional RBPs that participate across multiple mRNA life-cycle steps. We characterize the novel interactions and functions of different classes of multi-functional proteins. We find the scaffolding protein, ERH, interacts with numerous nuclear speckle proteins and facilitates splicing and mRNA export. Finally, we show that the splicing factor, SNRNP200, interacts with nuclear export, localization, and translation proteins and is an essential factor of RNA granule formation during stress. Our large-scale RBP interaction network provides new insights and a valuable resource for exploring new RBP complexes operating to control gene expression.
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