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Cell type-specific ribosome profiling in vivo.

ABSTRACT: Cell type-specific ribosome profiling in vivo.

PROVIDER: PRJNA223060 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1013470.fastq.gz	Fastqsanger.gz
	SRR1013480.fastq.gz	Fastqsanger.gz
	SRR1013471.fastq.gz	Fastqsanger.gz
	SRR1013481.fastq.gz	Fastqsanger.gz
	SRR1013472.fastq.gz	Fastqsanger.gz

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Cell type-specific ribosome profiling in vivo.

Project description:Cell type-specific ribosome profiling in vivo.

| PRJNA223060 | ENA

Cell type-specific ribosome profiling in vivo.

Project description:We report cell-type specific ribosome profiling in a mouse glioma model. We report a strategy for cell-type specific ribosome profiling in vivo. Our strategy was applied to the characterization of a mouse glioma model.

2014-08-25 | E-GEOD-51424 | biostudies-arrayexpress

Cell type-specific ribosome profiling in vivo.

Project description:We report cell-type specific ribosome profiling in a mouse glioma model.

2014-08-25 | GSE51424 | GEO

Cell-type-specific gene expression profiling using ribosome affinity purification

Project description:Post-transcriptional regulation including mRNA binding to ribosomes plays an important role in determining cell-type-specific gene expression patterns. Here, we applied an approach that profiles cell-type-specific mRNAs. The Translating Ribosome Affinity Purification method (TRAP; Heiman et al., Cell, 2008 and Doyle et al., Cell, 2008) was developed in mice and has been combined with the UAS/Gal4 system in Drosophila (Thomas et al., PLoS ONE, 2012). TRAP is a powerful method to find cell-type-specific differences at the level of the 'translatome' (Dougherty, Schmidt, Nakajima, & Heintz, Nucleic Acids Research, 2010). In parallel to published efforts, we developed and implemented the method for the fly and compared distinct head cell types and identified cell-type-specific transcript classes with neuronal (e.g. receptor-, neuropeptide- or hormone activity) or glial function (e.g. transporter activity). Neuronal TRAP genes are over-represented in the brain, larval CNS and thoracico-abdominal ganglion (Chintapalli, Wang, & Dow, Nature Genetics, 2007). Using cell-type-to-cell-type comparisons (e.g. neurons vs. glia), instead of a given cell population to the total (e.g. neurons vs. head), the differences could be identified with greater resolution. TRAP uncovered more neuronal genes compared to neuronal RNA polymerase II ChIP-seq data (Schauer et al., Cell Reports, 2013). Thus, TRAP data confirm the importance of post-transcriptional regulation in defining cell identity. TRAP is one of the best methods to reveal differential "omics" data among distinct cell types by profiling ribosome-bound mRNAs. TRAP is a promising tool to reveal cell-type-specific transcriptional and translational changes in a perturbed environment.

2017-02-01 | GSE89993 | GEO

Ligation-Free Ribosome Profiling Reveals Cell Type-Specific Regulation of Protein Synthesis in the Brain

Project description:Ribosome profiling has emerged as a powerful tool for genome-wide measurements of translation, but library construction requires multiple ligation steps and remains cumbersome relative to more conventional deep sequencing experiments. We report a new approach to ribosome profiling that does not require ligation. Library construction for ligation-free ribosome profiling can be completed in one day with as little as 1 ng of purified RNA footprints. We used ligation-free ribosome profiling to identify new patterns of cell type-specific translation in the brain and tested its ability to identify translational targets of mTOR signaling in the brain.

2016-06-07 | GSE78163 | GEO

Cell type- and replication stage-specific influenza virus responses in vivo

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Epidermal basal cell-specific in vivo ribosome profiling to describe the translation landscape of HrasG12V and Eif2b5

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Ribosome Profiling of mouse skin squamous tumours

Project description:Purpose: Ribosome profiling has revolutionized systems-based analysis and which produces a âglobal snapshotâ of all the ribosomes translationally active in a cell at a particular moment. The goals of this study are to first apply ribosome profiling to in vivo samples for the first time and in particular to stem cells and tumours and second to determine which mRNAs are being actively translated in these particular situations. Although much is known about gene expression regulation, little is known about how protein translation regulation can affect stem cell differentiation and tumour progression. Methods: several replicates of ribosome and mRNA profiles of wild-type (WT) and NSun2 -/- mouse skin squamous tumours were generated by deep sequencing, using Illumina HiSeq platform. Results: Our analyses reveal that activation of stress response pathways in vivo drives both a global reduction of protein synthesis and altered translation of specific mRNAs that together promote stem cell functions and tumourigenesis. Ribosome profiles of wild-type (WT) and NSun2 -/- mouse skin squamous tumours

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2017-11-10 | PXD007703 | Pride

Analysing the effect of cellular energy levels on codon-specific ribosome occupancy in vivo

Project description:Analysing the effect of cellular energy levels on codon-specific ribosome occupancy in vivo

| PRJNA894167 | ENA