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Dataset results
33 results for “secondary RNA structure”
The datasets used in "RNA secondary structure prediction using deep learning with thermodynamic integration"
<p>The datasets used in "RNA secondary structure prediction using deep learning with thermodynamic integration"</p>
Structural 3D domain reconstruction of the RNA genome from viruses from a secondary structure model
<p>Fragments and final models of reconstructed STMV genome from in virio and in vitro secondary structures reported in Larman et al. (2017).</p> <p>Simulation scripts for simulations of genome and fragments.</p> <p>Full code of SPQR package for performing simulations.</p>
Data from: Compensatory evolution in RNA secondary structures increases substitution rate variation among sites
There is growing evidence that interactions between biological molecules (e.g., RNA-RNA, protein-protein, RNA-protein) place limits on the rate and trajectory of molecular evolution. Here, by extending Kimura's model of compensatory evolution at interacting sites, we show that the ratio of transition to transversion substitutions (κ) at interacting sites should be equal to the square of the ratio at independent sites. Because transition mutations generally occur at a higher rate than transversions, the model predicts that κ should be higher at interacting sites than at independent sites. We tested this prediction in 10 RNA secondary structures by comparing phylogenetically derived estimates of κ in paired sites within stems (κ(p)) and unpaired sites within loops (κ(u)). Eight of the 10 structures showed an excellent match to the quantitative predictions of the model, and 9 of the 10 structures matched the qualitative prediction κ(p) > κ(u). Only the Rev response element from the human immunovirus (HIV) genome showed the reverse pattern, with κ(p) < κ(u). Although a variety of evolutionary forces could produce quantitative deviations from the model predictions, the reversal in magnitude of κ(p) and κ(u) could be achieved only by violating the model assumption that the underlying transition (or transversion) mutation rates were identical in paired and unpaired regions of the molecule. We explore the ability of the APOBEC3 enzymes, host defense mechanisms against retroviruses, which induce transition mutations preferentially in single-stranded regions of the HIV genome, to explain this exception to the rule. Taken as a whole, our findings suggest that kappa may have utility as a simple diagnostic to evaluate proposed secondary structures.
Data from: Compensatory evolution in RNA secondary structures increases substitution rate variation among sites
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Global Analysis of the RNA-Protein Interaction and RNA Secondary Structure Landscapes Identifies Dynamic Changes During Mammalian Erythropoiesis (mRNA)
GEO Series GSE148421. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Landscape and variation of RNA secondary structure across the human transcriptome
GEO Series GSE50676. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing; Other.
Genome-wide Measurement of RNA Secondary Structure in Yeast
GEO Series GSE22393. Saccharomyces cerevisiae. 7 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome
GEO Series GSE54106. Mus musculus. 7 samples. Type: Other; Expression profiling by high throughput sequencing.
In vivo atlas of RNA secondary structures recognized by ADARs [RNA-Seq]
GEO Series GSE136326. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
N6-methyladenosine and RNA secondary structure affect transcript stability and translation during systemic salt stress in Arabidopsis
GEO Series GSE147812. Arabidopsis thaliana. 16 samples. Type: Other.
Genome-wide Identification of DEAD-box RNA Helicase Targets Reveals Roles for RNA Secondary Structure Remodeling in mRNA Processing (RNA Pol II ChIP-seq)
GEO Series GSE125283. Saccharomyces cerevisiae. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis
GEO Series GSE247244. Homo sapiens; Escherichia coli. 29 samples. Type: Other; Expression profiling by high throughput sequencing.
In vivo atlas of RNA secondary structures recognized by ADARs [irCLASH-seq&hiCLIP-seq]
GEO Series GSE136325. Homo sapiens. 11 samples. Type: Other.
Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus
GEO Series GSE58974. Arabidopsis thaliana. 10 samples. Type: Expression profiling by high throughput sequencing; Other.
Genome-wide Identification of DEAD-box RNA Helicase Targets Reveals Roles for RNA Secondary Structure Remodeling in mRNA Processing (Structure-seq)
GEO Series GSE106478. Saccharomyces cerevisiae. 10 samples. Type: Other.
Global Analysis of the RNA-Protein Interaction and RNA Secondary Structure Landscapes Identifies Dynamic Changes During Mammalian Erythropoiesis
GEO Series GSE142242. Mus musculus. 24 samples. Type: Other.
Genome-wide Identification of DEAD-box RNA Helicase Targets Reveals Roles for RNA Secondary Structure Remodeling in mRNA Processing
GEO Series GSE106479. Saccharomyces cerevisiae. 28 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing.
In-cell RNA secondary structure analysis of functional SINE transcripts
GEO Series GSE224534. Homo sapiens. 16 samples. Type: Other.
LinearCoFold and LinearCoPartition: Linear-Time Algorithms for Secondary Structure Prediction of Interacting RNA molecules
<p>LinearCoFold and LinearCoPartition</p>
In vivo atlas of RNA secondary structures recognized by ADARs
GEO Series GSE136327. Homo sapiens. 23 samples. Type: Expression profiling by high throughput sequencing; 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.
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.