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40 results for “RNA folding”
Characterizing the Folding Transition State Ensembles in the Energy Landscape of an RNA Tetraloop - available data.
<p>Trajectory file and scripts necessary to generate an ELViM [Oliveira, A. B.; Yang, H.; Whitford, P. C.; Leite, V. B. P. JCTC, 2019, 15, p.6482] projection of the conformational space for the GCAA tetraloop.</p>
Supplemental Data for "Shape changes and cooperativity in the folding of central domain of the 16S ribosomal RNA"
<p>This is data set associated with an article "Shape changes and cooperativity in the folding of central domain of the 16S ribosomal RNA" by Naoto Hori, Natalia A. Denesyuk, and D. Thirumalai. See README.txt file for the format of the data set.</p>
Dataset to manuscript "Trans-cis isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells" accepted for publication in Nucleic Acids Research
<p><strong>This folder contains all raw data underlying the results presented in a manuscript, accepted for publication in Nucleic Acids Research, and entitled:</strong></p> <p> </p> <p><strong><em>Trans</em></strong><strong>-<em>cis</em> isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells </strong></p> <p> </p> <p><strong>Authored by:</strong></p> <p>Akira Kitamura<sup>2,*</sup>, Johan Tornmalm<sup>1,*</sup>, Baris Demirbay<sup>1</sup>, Joachim Piguet<sup>1</sup>, Masataka Kinjo<sup>2</sup>, Jerker Widengren<sup>1+</sup></p> <p> </p> <p><sup>1</sup> Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm, Sweden</p> <p><sup>2</sup> Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan</p> <p><sup>* </sup>Contributed equally</p> <p><sup>+</sup> To whom correspondence should be addressed. Email: jwideng@kth.se. Tel: +46-8-7907813</p> <p> </p> <p><strong>The data files are grouped into the different techniques used to generate them, and refer to the figures/tables in the manuscript where the extracted results are presented. </strong></p> <p> </p> <p><strong>ABSTRACT</strong></p> <p>Guanine (G)-rich nucleic acids are prone to assemble into four-stranded structures, so-called G-quadruplexes. Abnormal GGGGCC repeat elongations, and in particular their folding states, are associated with amyotrophic lateral sclerosis and frontotemporal dementia. Due to methodological constraints however, most studies of G quadruplex structures are restricted to <em>in vitro</em> conditions. Evidence of how GGGGCC repeats form into G-quadruplexes <em>in vivo</em> is sparse. We devised a readout strategy, exploiting the sensitivity of <em>trans</em>-<em>cis</em> isomerization of cyanine dyes to local viscosity and sterical constraints. Thereby, folding states of cyanine-labeled RNA, and in particular G-quadruplexes, can be identified in a sensitive manner. The isomerization kinetics, monitored via fluorescence blinking generated upon transitions between a fluorescent <em>trans</em> isomer and a non-fluorescent <em>cis</em> isomer, was first characterized for RNA with GGGGCC repeats in aqueous solution using fluorescence correlation spectroscopy and transient state (TRAST) monitoring. With TRAST, monitoring the isomerization kinetics from how the average fluorescence intensity varies with laser excitation modulation characteristics, we could then detect folding states of fluorescently tagged RNA introduced into live cells.</p>
Data - Synthetic mammalian RNA-based gene circuits for high fold change expression
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single-molecule tertiary structure determination reveals RNA folding landscape
<p>Initial release of the 6HB RNA origami 3D density maps, fitting models and EMDB validation reports.</p>
Data from: Protein-mediated RNA folding governs sequence-specific interactions between rotavirus genome segments
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G-quadruplex folding in Xist RNA antagonizes PRC2 activity for step-wise regulation of X-chromosome inactivation
GEO Series GSE219083. Mus musculus. 36 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Genome-wide measurement of RNA folding energies
GEO Series GSE39680. Saccharomyces cerevisiae. 10 samples. Type: Expression profiling by high throughput sequencing; Other.
Spatial chromosome folding and active transcription drive DNA fragility and formation of oncogenic MLL translocations [RNA-Seq]
GEO Series GSE121741. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
RNA-Seq of vocal folds of rabbits exposed to a low relative humidity environment
GEO Series GSE148588. Oryctolagus cuniculus. 12 samples. Type: Expression profiling by high throughput sequencing.
HMGB1 coordinates SASP-related chromatin folding and RNA homeostasis on the path to senescence [RNA-seq]
GEO Series GSE171779. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Stress promotes RNA G-quadruplex folding in human cells
GEO Series GSE200706. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Epigenetic regulation by dynamic RNA G-quadruplex folding and unfolding (DMS-Seq)
GEO Series GSE219079. Mus musculus. 6 samples. Type: Other.
Extensive folding variability between homologous chromosomes in mammalian cells [RNA-seq]
GEO Series GSE254675. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
RNA-sequencing demonstrates transcriptional differences between human vocal fold fibroblasts and myofibroblasts
GEO Series GSE278852. Homo sapiens. 14 samples. Type: Expression profiling by array.
Alteration of genome folding via engineered transposon insertion [RNA-seq]
GEO Series GSE137374. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
HMGB1 coordinates SASP-related chromatin folding and RNA homeostasis on the path to senescence
GEO Series GSE171782. Homo sapiens. 32 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Data Sharing for: ''RNA folding landscapes from explicit solvent all-atom simulations"
<p>Data required to reproduce the figures and analysis in the paper: ''RNA folding landscapes from explicit solvent all-atom simulations".</p>
Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors [RNA-seq]
GEO Series GSE196449. Homo sapiens. 34 samples. Type: Expression profiling by high throughput sequencing.
HMGB1 coordinates SASP-related chromatin folding and RNA homeostasis on the path to senescence [Ribo-seq]
GEO Series GSE171780. Homo sapiens. 12 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)
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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.