Integrative analysis of RNA-seq and Ribo-seq reveals that lncRNA regulates chicken myogenesis through encoding peptide [PDF]
Journal of Animal Science and BiotechnologyBackground Long noncoding RNAs (lncRNAs) participate in various critical regulatory steps during myogenesis. LncRNAs can encode small peptides, which can regulate gene expression through multiple mechanisms, thereby participating in key biological ...
Yufang Niu +12 more
doaj +2 more sources
Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions [PDF]
Nature CommunicationsThe mesophilic methanogenic archaeal model organism Methanosarcina mazei strain Gö1 is crucial for climate and environmental research due to its ability to produce methane. Here, we establish a Ribo-seq protocol for M.
Muhammad Aammar Tufail +11 more
doaj +2 more sources
What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome? [PDF]
Molecular and Cellular Proteomics, 2023 Jennifer G Abelin +2 more
exaly +2 more sources
A tool for analyzing and visualizing ribo-seq data at the isoform level. [PDF]
BMC Bioinformatics, 2021 Abstract Background Translational regulation is one important aspect of gene expression regulation. Dysregulation of translation results in abnormal cell physiology and leads to diseases. Ribosome profiling (RP), also called ribo-seq, is a powerful experimental technique to study translational regulation.
Wu WS +5 more
europepmc +6 more sources
STATR: A simple analysis pipeline of Ribo-Seq in bacteria. [PDF]
J Microbiol, 2020 Gene expression changes in response to diverse environmental stimuli to regulate numerous cellular functions. Genes are expressed into their functional products with the help of messenger RNA (mRNA). Thus, measuring levels of mRNA in cells is important to understand cellular functions. With advances in next-generation sequencing (NGS), the abundance of
Choe D, Palsson B, Cho BK.
europepmc +3 more sources
InspectorORF: a tool for visualizing Ribo-Seq and additional genomic or transcriptomic data. [PDF]
Bioinform AdvAbstract Motivation The advent of ribosome profiling (an adaptation of RNA sequencing) to determine the translatome, has led to a huge improvement in our understanding of what parts of the transcriptome are translated. Many alternative open reading frames (ORFs) are now regularly being detected
Ward EL +4 more
europepmc +4 more sources
Identifying and Visualizing Novel Small Open Reading Frames (sORFs) via Ribo-Seq, Transcriptome Assembly, and ggRibo [PDF]
Methods in Molecular BiologyPolly Yingshan Hsu, Hsin-Yen Larry Wu
exaly +2 more sources
The Translatome Map: RNC-Seq vs. Ribo-Seq for Profiling of HBE, A549, and MCF-7 Cell Lines [PDF]
International Journal of Molecular SciencesAnna Kozlova +2 more
exaly +2 more sources
How tailored Ribo-seq methods probe unique translation events. [PDF]
RNARibosome profiling (Ribo-seq) is a next-generation, high-resolution sequencing technique that captures ribosome-protected mRNA fragments to map ribosome positions across the transcriptome. This method serves as a powerful proxy for global translational activity by revealing where ribosomes engage with mRNAs. Recent advances have expanded the utility of
Marks J, Meydan S.
europepmc +3 more sources
Trips-Viz: a transcriptome browser for exploring Ribo-Seq data. [PDF]
Nucleic Acids Res, 2019 Ribosome profiling (Ribo-Seq) is a technique that allows for the isolation and sequencing of mRNA fragments protected from nuclease digestion by actively translating ribosomes. Mapping these ribosome footprints to a genome or transcriptome generates quantitative information on translated regions.
Kiniry SJ +3 more
europepmc +5 more sources