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350 results for “Ribosome profiling”
The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation
<p>Additional files, Scripts and Data related to the manuscript Papadopoulos et al, The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation. </p> <p>Additional file 1: contains supplemental figures and tables of the manuscript</p> <p>Additional file 2: contains the complete list of the 89 Ribo-Seq datasets (89 biological replicas).</p> <p>Papadopoulos_et_al_2024.tar.gz: contains the scripts, raw data, intermediate data and final (processed) data to reproduce the analyses, Figures, and Tables of the manuscript Papadopoulos et al, The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation. </p> <p>The archive contains 3 directories:</p> <p>*** input: contains the protocols, raw data, and the associated intermediate processed data that are used as inputs of the scripts that perform the subsequent analyses and generate the Figures and Tables</p> <p><br>*** scripts: all the scripts necessary to perform the analyses of the manuscript and generate the final data, Figures and Tables available in the ./output directory</p> <p>*** output: contains the final processed data including the final lists and tables resulting from MSMS analyses or RiboSeq analyses, the final Figures and Tables of the manuscript as well as the 3 final tables that integrate the processed data from Ribo-Seq, MSMS, evolutionary analyses, sequence and structural analyses, final analyses on codon propensities. These 3 tables, beyond being necessary for the anlayses performed for this study can also be useful for users to realize their own analyses. All the data, Figures and Tables contained in this directory can be directly generated from the scripts available in the directory ./scripts and the data contained in the directory ./input. Please see the README in the different directories to reproduce everything.</p> <p> </p>
mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA gene
<p>mTAGs is a tool for the taxonomic profiling of metagenomes. It detects sequencing reads belonging to the small subunit of the ribosomal RNA (SSU-rRNA) gene and annotates them through the alignment to full-length degenerate consensus SSU-rRNA reference sequences. The tool is capable of processing single-end and pair-end metagenomic reads, takes advantage of the information contained in any region of the SSU-rRNA gene and provides relative abundance profiles at multiple taxonomic ranks (Domain, Phylum, Class, Order, Family, Genus and OTUs defined at a 97% sequence identity cutoff).</p>
Data from: Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster
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Ribosome profiling reveals a functional role for autophagy in protein translational control
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Data from: Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis
Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Because ribosomes decode mRNA every 3 nt, the periodic property of ribosome footprints could be used to identify novel translated ORFs. However, due to the limited resolution of existing methods, the 3-nt periodicity is observed mostly in a global analysis, but not in individual transcripts. Here, we report a protocol applied to Arabidopsis that maps over 90% of the footprints to the main reading frame and thus offers super-resolution profiles for individual transcripts to precisely define translated regions. The resulting data not only support many annotated and predicted noncanonical translation events but also uncover small ORFs in annotated noncoding RNAs and pseudogenes. A substantial number of these unannotated ORFs are evolutionarily conserved, and some produce stable proteins. Thus, our study provides a valuable resource for plant genomics and an efficient optimization strategy for ribosome profiling in other organisms.
Data from: Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis
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Ribosome profiling data obtained from HEK293T cells 30 minutes after treatment with arsenite to a final concentration of 40 µM
GEO Series GSE55195. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing; Other.
Proximity-specific ribosome profiling reveals the logic of localized mitochondrial translation
GEO Series GSE300977. Homo sapiens. 26 samples. Type: Other; Expression profiling by high throughput sequencing.
Decoding human cytomegalovirus using ribosome profiling
GEO Series GSE41605. Human betaherpesvirus 5. 16 samples. Type: Expression profiling by high throughput sequencing.
Ribosome profiling of HSV-1 infected cells
GEO Series GSE128322. Human alphaherpesvirus 1 strain 17; Homo sapiens. 10 samples. Type: Other.
Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments
GEO Series GSE136940. Schizosaccharomyces pombe; Candida albicans; Homo sapiens; Saccharomyces cerevisiae. 33 samples. Type: Expression profiling by high throughput sequencing.
High resolution view of bacteriophage lambda gene expression by ribosome profiling
GEO Series GSE47509. Escherichia coli str. K-12 substr. MG1655. 20 samples. Type: Expression profiling by high throughput sequencing.
Ribosome profiling reveals an important role for translational control in circadian gene expression
GEO Series GSE56924. Homo sapiens. 96 samples. Type: Expression profiling by high throughput sequencing; Other.
Transcription Factor Substitution during the Evolution of Fungal Ribosome Regulation_expression profiling
GEO Series GSE10499. Candida albicans. 12 samples. Type: Expression profiling by array.
Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames
GEO Series GSE67305. Mus musculus. 48 samples. Type: Expression profiling by high throughput sequencing.
Ligation-Free Ribosome Profiling Reveals Cell Type-Specific Regulation of Protein Synthesis in the Brain
GEO Series GSE78163. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing; Other.
Testing conditions for ribosome profiling in Drosophila melanogaster
GEO Series GSE166408. Drosophila melanogaster. 5 samples. Type: Other.
Ribosome profiling in DDX3X degron cell lines and complementation with sex-linked paralogs
GEO Series GSE180669. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing; Other.
Hippocampal neurons’ cytosolic and membrane-bound ribosomal transcript profiles are differentially regulated by learning and subsequent sleep
GEO Series GSE216163. Mus musculus. 180 samples. Type: Expression profiling by high throughput sequencing.
Translation Inhibitors Cause Abnormalities in Ribosome Profiling Experiments
GEO Series GSE59573. Saccharomyces cerevisiae. 24 samples. Type: Other.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.