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199 results for “translatome”
Transcriptome, metaranscriptome, and translatome data for RIBOSS
<p>This record contains long- and short-read sequence alignment files to test <a href="https://github.com/lcscs12345/riboss">RIBOSS</a>.</p> <p>To reproduce the results in <a href="https://github.com/lcscs12345/riboss_paper/blob/master/jupyter_notebooks/styphimurium.ipynb">styphimurium.ipynb</a>, clone the <a href="https://github.com/lcscs12345/riboss_paper">RIBOSS_paper</a> repository, and create a <code>conda</code> environment according to <code>README</code>.</p> <p>Create new directories <code>mkdir -p doc/ doc/metatranscriptome doc/styphimurium/ doc/styphimurium/rnaseq doc/styphimurium/riboseq</code>.</p> <p>Download the alignment files for <em>S. enterica</em> transcriptome and metatranscriptome (a cocktail of <em>S. enterica</em> serovar Enteritidis, <em>Escherichia coli</em> O157:H7, and <em>Listeria monocytogenes</em>).</p> <ul> <li>SRR11215003.bam and SRR11215004.bam: Nanopore long-read direct RNA-seq. Download and <code>mv SRR24781620.bam doc/metatranscriptome</code>.</li> <li>SRR11215663.bam and SRR11215664.bam: Illumina short-read RNA-seq. Download and <code>mv SRR24781620.bam doc/metatranscriptome</code>.</li> <li>SRR24781620.bam: Nanopore long-read cDNA sequencing. Download and <code>mv SRR24781620.bam doc/styphimurium/rnaseq</code>.</li> </ul> <p>Download <em>S. enterica</em> serovar Typhimurium ribosome profiling data and <code>mv ERR913094*.out.bam doc/styphimurium/riboseq</code>.</p> <ul> <li><code>ERR9130942Aligned.out.bam</code>: RNase I, 1000 U.</li> <li><code>ERR9130943Aligned.out.bam</code>: RNase I, 500 U.</li> <li><code>ERR9130946Aligned.out.bam</code>: matched RNA-seq.</li> </ul>
Annotation of the non-canonical translatome reveals that CHO cell microproteins are a new class of therapeutic antibody drug product impurity
<p>3,681 novel Chinese hamster proteoforms (derived from uORFs, ouORFs and ORFs encoded on NCBI annotated non-coding RNAs).</p>
Gene expression dataset of the Spatially Resolved Single-cell Translatomics at Molecular Resolution
<p>Here are the gene expression datasets of RIBOmap included in "<strong>Spatially Resolved Single-cell Translatomics at Molecular Resolution</strong>" from Zeng et al. Please refer to the README file for more detailed information. </p> <p> </p> <p><strong>Abstract</strong></p> <p>The precise control of mRNA translation is a crucial step in post-transcriptional gene regulation of cellular physiology. However, it remains a major challenge to systematically study mRNA translation at the transcriptomic scale with spatial and single-cell resolution. Here, we report the development of RIBOmap, a three-dimensional (3D) in situ profiling method to detect mRNA translation of thousands of genes simultaneously in intact cells and tissues. By applying RIBOmap to 981 genes in HeLa cells, we revealed a remarkable dependency of translation on cell-cycle stages and subcellular localization. Furthermore, we profiled single-cell translatomes of 5,413 genes in adult mouse brain tissues yielding a spatial cell atlas of 119,173 cells. The pairwise spatial mapping of single-cell translatome and transcriptome in two adjacent mouse brain slices revealed cell-type and brain-region-dependent translational regulation and suggested a translation remodeling during oligodendrocyte lineage maturation. The spatial translatome profiling detected widespread patterns of localized translation in neuronal and glial cells in intact brain tissue networks. Together, RIBOmap presents the first spatially resolved single-cell translatomics technology, accelerating our understanding of protein synthesis in the context of subcellular architecture, cell types, and tissue anatomy.</p>
Preprocessed dataset of the Spatially Resolved Single-cell Translatomics at Molecular Resolution
<p>Here are the pre-processed image datasets of RIBOmap included in "<strong>Spatially Resolved Single-cell Translatomics at Molecular Resolution</strong>" from Zeng et al. Please refer to the README file for more detailed information. </p> <p> </p> <p><strong>Abstract</strong></p> <p>The precise control of mRNA translation is a crucial step in post-transcriptional gene regulation of cellular physiology. However, it remains a major challenge to systematically study mRNA translation at the transcriptomic scale with spatial and single-cell resolution. Here, we report the development of RIBOmap, a three-dimensional (3D) in situ profiling method to detect mRNA translation of thousands of genes simultaneously in intact cells and tissues. By applying RIBOmap to 981 genes in HeLa cells, we revealed a remarkable dependency of translation on cell-cycle stages and subcellular localization. Furthermore, we profiled single-cell translatomes of 5,413 genes in adult mouse brain tissues yielding a spatial cell atlas of 119,173 cells. The pairwise spatial mapping of single-cell translatome and transcriptome in two adjacent mouse brain slices revealed cell-type and brain-region-dependent translational regulation and suggested a translation remodeling during oligodendrocyte lineage maturation. The spatial translatome profiling detected widespread patterns of localized translation in neuronal and glial cells in intact brain tissue networks. Together, RIBOmap presents the first spatially resolved single-cell translatomics technology, accelerating our understanding of protein synthesis in the context of subcellular architecture, cell types, and tissue anatomy.</p>
Example data and pretrained Translatomer model
Open the record for dataset details and reuse information.
Phloem associated foliar translatomes in Prunus domestica L.
GEO Series GSE111738. Prunus domestica. 27 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome and translatome of Streptomyces avermitilis MA-4680
GEO Series GSE118597. Streptomyces avermitilis. 22 samples. Type: Expression profiling by high throughput sequencing; Other.
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.
Effects of astrocytic absence of glucose transporter 1 (GLUT1) on the cortical astrocytic translatome
GEO Series GSE223687. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing; Other.
Next generation sequencing analysis of control and KSR1 knockdown CRC cell line translatomes.
GEO Series GSE164492. Homo sapiens. 24 samples. Type: Expression profiling by high throughput sequencing.
Effect of N1-acetylspermidine treatment on the translatome of hair follicle stem cell organoid cultures
GEO Series GSE164806. Mus musculus. 16 samples. Type: Expression profiling by high throughput sequencing; Other.
Genome-wide profilings of transcriptome and translatome in mouse hippocampi after contextual fear conditioning
GEO Series GSE72064. Mus musculus. 34 samples. Type: Expression profiling by high throughput sequencing; Other.
Translatome analysis of Mycobacterium tuberculosis
GEO Series GSE151718. Mycobacterium tuberculosis. 6 samples. Type: Other.
Genome-wide transcriptomic and translatomic profiling in halofuginone and vehicle treated mouse fibroblasts
GEO Series GSE136838. Mus musculus. 24 samples. Type: Expression profiling by high throughput sequencing.
Translatome analysis of the ribosomal protein L10 R98S mutation reveals altered serine metabolism in acute lymphoblastic leukemia [supplementaryRNA-seq]
GEO Series GSE106530. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Comprehensive Analysis of the Translatome in High Fat Diet-Induced Liver Steatosis
GEO Series GSE146627. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome (RNA-Seq), translatome (Ribo-Seq), and YB-1/YB-3-bound mRNAs (RIP-Seq) of HEK293T, HEK293TdeltaYB-1, and HEK293T+HA-YB-1 cells
GEO Series GSE130781. Homo sapiens. 41 samples. Type: Expression profiling by high throughput sequencing.
Translatome profiling of warm temperature (35°C -> 38.5°C) treated mouse embryonic fibroblast cells in the presense or absence of PI3K inhibitor, 17β-hydroxy wortmannin
GEO Series GSE211532. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Translatome analysis in postmortem brain-derived samples from Autism Spectrum Disorder affected individuals
GEO Series GSE236761. Homo sapiens. 20 samples. Type: Expression profiling by high throughput sequencing.
Translatome and transcriptome profiling of SH-SY5Y cells treated with sublytic doses of staphylococcal alpha-hemolysin
GEO Series GSE50652. Homo sapiens. 12 samples. Type: Expression profiling by array.
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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.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.