Results 151 to 160 of about 168,078 (169)
Beyond Read-Counts: Ribo-seq Data Analysis to Understand the Functions of the Transcriptome
Trends in Genetics, 2017 By mapping the positions of millions of translating ribosomes in the cell, ribosome profiling (Ribo-seq) has established its role as a powerful tool to study gene expression. Several laboratories have introduced modifications to the experimental protocol
Uwe Ohler, Lorenzo Calviello
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A Ribo-Seq Method to Study Genome-Wide Translational Regulation in Plants
Methods in Molecular Biology, 2022Protein production from mRNA is one of the fundamental molecular processes in a cell. Accurate genome-wide information on the levels of translation and ribosome distribution on mRNA can be gathered by carrying out ribosome footprinting, aka Ribo-seq.
José Alonso, Anna Stepanova
exaly +3 more sources
Single-cell Ribo-seq reveals cell cycle-dependent translational pausing
Nature, 2021Single-cell sequencing methods have enabled in-depth analysis of the diversity of cell types and cell states in a wide range of organisms. These tools focus predominantly on sequencing the genomes1, epigenomes2 and transcriptomes3 of single cells. However, despite recent progress in detecting proteins by mass spectrometry with single-cell resolution4 ...
Michael Vaninsberghe +2 more
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RiboSimR: A Tool for Simulation and Power Analysis of Ribo-seq Data
2020RNA-seq and Ribo-seq are widespread quantitative methods for assessing transcription and translation. They can be used to detect differential expression, differential translation, and differential translation efficiency between conditions. The statistical power to detect differential genes is affected by multiple factors, such as the number of ...
Patrick Perkins +3 more
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Poly-A Tailing and Adaptor Ligation Methods for Ribo-Seq Library Construction
2021Ribosome profiling is a powerful technique that enables researchers to monitor translational events across the transcriptome. It provides a snapshot of ribosome positions and density across the transcriptome at a sub-codon resolution. Here we describe the whole procedure of profiling ribosome footprints in mammalian cells.
Jingfan, Qiu, Shu-Bing, Qian
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RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
Journal of Visualized Experiments, 2021The ribosome profiling technique (RIBO-seq) is currently the most effective tool for studying the process of protein synthesis in vivo. The advantage of this method, in comparison to other approaches, is its ability to monitor translation by precisely mapping the position and number of ribosomes on a mRNA transcript.
Kopik, Natalia +4 more
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Journal of Genetics and Genomics
Translation is a crucial step in gene expression. Over the past decade, the development and application of ribosome profiling (Ribo-seq) have significantly advanced our understanding of translational regulation in vivo. However, the analysis and visualization of Ribo-seq data remain challenging. Despite the availability of various analytical pipelines,
Shuchao Ren, Zhipeng Zhou
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Translation is a crucial step in gene expression. Over the past decade, the development and application of ribosome profiling (Ribo-seq) have significantly advanced our understanding of translational regulation in vivo. However, the analysis and visualization of Ribo-seq data remain challenging. Despite the availability of various analytical pipelines,
Shuchao Ren, Zhipeng Zhou
exaly +3 more sources
A Versatile Ribo-seq Workflow for Enhanced Analysis of Ribosome Dynamics
Ribosome profiling (or ribo-sequencing) is a powerful technique that enables high-resolution analysis of active translation by sequencing ribosome-protected mRNA fragments. Developed in 2009 by Nicholas Ingolia and Jonathan Weissman, it provides direct insights into which mRNAs are being translated and at what rate, surpassing traditional ...Hélène, Hérault +2 more
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Ribo-seq analysis of B16/F10 WT and Ythdf1 KO group
2022To identify the efficiency of downstream translation regulated by Ythdf1 in an m6A-dependent manner, we performed Ribo-seq analysis of WT and Ythdf1 KO group.
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