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Mus musculus

ABSTRACT: Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes

PROVIDER: PRJNA144149 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR315591.fastq.gz	Fastqsanger.gz
	SRR315592.fastq.gz	Fastqsanger.gz
	SRR315593.fastq.gz	Fastqsanger.gz
	SRR315594.fastq.gz	Fastqsanger.gz
	SRR315595.fastq.gz	Fastqsanger.gz

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Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes

Project description:The ability to sequence genomes has far outstripped approaches for deciphering the information they encode. Here we present a suite of techniques, based on ribosome profiling (the deep-sequencing of ribosome-protected mRNA fragments), to provide genome-wide maps of protein synthesis as well as a pulse-chase strategy for determining rates of translation elongation. We exploit the propensity of harringtonine to cause ribosomes to accumulate at sites of translation initiation together with a machine learning algorithm to define protein products systematically. Analysis of translation in mouse embryonic stem cells reveals thousands of strong pause sites and novel translation products. These include amino-terminal extensions and truncations and upstream open reading frames with regulatory potential, initiated at both AUG and non-AUG codons, whose translation changes after differentiation. We also define a new class of short, polycistronic ribosome-associated coding RNAs (sprcRNAs) that encode small proteins. Our studies reveal an unanticipated complexity to mammalian proteomes. Examination of translation in mouse embryonic stem cells and during differentiation into embryoid bodies

2011-11-03 | E-GEOD-30839 | biostudies-arrayexpress

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes

2011-11-03 | GSE30839 | GEO

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Project description:A regression-based analysis of ribosome-profiling data reveals a conserved complexity to mammalian translation

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Ribosome profiling with translation inhibitors reveals pervasive translation in murine ES cells

Project description:Ribosome profiling with translation inhibitors reveals pervasive translation in murine ES cells. Ribosome profiling or stranded RNAseq (ribominus) with murine embryonic stem cells treated with either DMD-pateamineA, Puromycin, Harringtonine or vehicle (no drug control). Two replicates per condition.

2016-01-12 | E-GEOD-67741 | biostudies-arrayexpress

Metabolomics Workbench ST000003 - GNPS - Metabolomic analysis of mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells

Project description:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis

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Project description:Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells [ribosome profiling]

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A regression-based analysis of ribosome-profiling data reveals a conserved complexity to mammalian translation

Project description:A fundamental goal of genomics is to identify the complete set of expressed proteins. Automated annotation strategies rely on assumptions about protein-coding sequences (CDSs), e.g., they are conserved, do not overlap, and exceed a minimum length. However, an increasing number of newly discovered proteins violate these rules. Here we present an experimental and analytical framework, based on ribosome profiling and linear regression, for systematic identification and quantification of translation. Application of this approach to lipopolysaccharide-stimulated mouse dendritic cells and HCMV-infected human fibroblasts identifies thousands of novel CDSs, including micropeptides and variants of known proteins, that bear the hallmarks of canonical translation and exhibit comparable translation levels and dynamics to annotated CDSs. Remarkably, many translation events are identified in both mouse and human cells even when the peptide sequence is not conserved. Our work thus reveals an unexpected complexity to mammalian translation suited to provide both conserved regulatory or protein-based functions. 37 ribosome footprint samples from mouse BMDCs across a time course of LPS stimulation and in the presence or absence of translation inhibitors cycloheximide, harringtonine, or lactimidomycin. A mock (non-LPS stimulated) time course is also included, collected in the presence of cycloheximide. Two replicates are available for the LPS timecourse under CHX treatment.

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Project description:Transcriptome profiling reveals novel Disabled-2-associated downstream effectors in mouse embryonic stem cells (ESC)

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Project description:Gene profiling of mouse embryonic stem cell subpopulations (CBX11)

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Project description:Foxp1 binding profiling in mouse embryonic neural stem cells (NSCs)

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