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Dataset results
63 results for “RNA motifs”
Double-stranded RNA structural elements holding the key to translational regulation in cancer: the case of editing in RNA Binding Motif Protein 8A
<p>Raw data supporting the manuscript</p> <p>Abukar, A.;Wipplinger, M.;<br> Hariharan, A.; Sun, S.; Ronner, M.;<br> Sculco, M.; Okonska, A.;<br> Kresoja-Rakic, J.; Rehrauer, H.; Qi, W.;<br> et al. Double-Stranded RNA<br> Structural Elements Holding the Key<br> to Translational Regulation in Cancer:<br> The Case of Editing in RNA-Binding<br> Motif Protein 8A. Cells 2021, 10, 3543.<br> https://doi.org/10.3390/<br> cells10123543</p>
Automated recognition of RNA structure motifs by their SHAPE data signatures
<p>Datasets, code and results supporting the manuscript:</p> <p>Radecki P., Ledda M. & Aviran S., Automated recognition of RNA structure motifs by their SHAPE data signatures</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.
<p>This repository contains the representative structures of the 20 clusters obtained, which constitute the “MD-adapted structure ensemble”: i.e., sets of atomic coordinates that capture the flexibility and the pre-miR20b (<a href="https://zenodo.org/api/files/ee12021f-4398-465a-9ff6-ddb7be32765f/ensemble_MD_2n7x.pdb?versionId=310a80f6-aa64-445d-8641-45faf9f1ac03">ensemble_MD_2n7x.pdb</a>) and Rbfox/pre-miR20b (<a href="https://zenodo.org/api/files/ee12021f-4398-465a-9ff6-ddb7be32765f/ensemble_MD_2n82.pdb?versionId=82d7afcb-8a92-4daa-8150-789dbd7b2474">ensemble_MD_2n82.pdb</a>) conformers suggested by MD simulations while still retaining the highest possible level of agreement with the primary NMR data.</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.-PART 8
<p>Simulations of the miR20b RNA with the Case vdW modification to amber force field and OPC water molecules.</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study- Part 3
<p>Trajectories and input files for the simulations of the Rbfox·pre-miR20b complex.</p>
Molecular basis for the increased affinity of an RNA recognition motif protein engineered to re-direct its specificity -PART 5
<p>Trajectories and input files for the simulations (REST2, REST2-PS and unbiased MD) of the Rbfox*·pre-miR20b* complex.</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study- PART 2
<p>Trajectories and input files of the simulations of the free pre-miR20b.</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study-PART 7
<p>Simulations of the Rbfox*-miR20b and of the Rbfox-mir20b* complexes.</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study- PART 6
<p>Trajectories and input files of the simulations of the S151T Rbfox*·pre-miR20b* system.</p>
Molecular basis for the increased affinity of an RNA recognition motif protein engineered to re-direct its specificity -PART 4
<p>Trajectory and input files for the simulation of the Rbfox* variant. </p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study- PART 1
<p>Simulations of the Rbfox protein.</p> <p> </p>
Interactive Structural Analysis of KH3-4 Didomains of IGF2BPs with Preferred RNA Motif Having m6A through Dynamics Simulation Studies
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A Point Mutation in the RNA Recognition Motif of CSTF2 Associated with Intellectual Disability in Humans Causes Defects in 3′ End Processing [3'prime-seq]
GEO Series GSE152975. Mus musculus. 8 samples. Type: Other.
RG/RGG boxes are common binding motifs in RNA-G-quadruplex-interacting proteins
GEO Series GSE106476. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
Expression and transcript isoform profiling of reprogramming cells expressing a Sox2 mutant lacking a putative RNA binding motif [PAR-CLIP]
GEO Series GSE115273. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Expression and transcript isoform profiling of reprogramming cells expressing a Sox2 mutant lacking a putative RNA binding motif
GEO Series GSE115452. Homo sapiens; Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing.
Pateamine A mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs
GEO Series GSE243312. Homo sapiens; synthetic construct. 36 samples. Type: Expression profiling by high throughput sequencing; Other.
Global Analysis of Glucocorticoid Receptor-Associated Transcripts and Identification of a Target RNA Motif
GEO Series GSE24748. Homo sapiens. 7 samples. Type: Other.
Direct identification of endogenous SMG6 targets and a preferred motif spanning SMG6 cleavage sites by parallel analysis of RNA ends in human cells
GEO Series GSE61398. Homo sapiens. 36 samples. Type: Expression profiling by high throughput sequencing; Other.
ZSCAN4-binding motif - TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes [RNA-Seq]
GEO Series GSE243627. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
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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.