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Dataset results
162 results for “rna 3d”
Smart 3D super-resolution microscopy reveals the architecture of the RNA scaffold in a nuclear body
<p>Data associated with the article "Smart 3D super-resolution microscopy reveals the architecture of the RNA scaffold in a nuclear body". A README.txt is provided that explains the data provided.</p>
RNA 3D structure modeling by fragment assembly with Small Angle X-ray Scattering restraints
<p>Structure determination is a key step in the functional characterization of many non-coding RNA molecules. High-resolution RNA 3D structure determination efforts, however, are not keeping up with the pace of discovery of new non-coding RNA sequences. This increases the importance of computational approaches and low-resolution experimental data, such as from the Small Angle X-ray Scattering experiments. We present RNA Masonry, a computer program and a web service for a fully automated modeling of RNA 3D structures. It assemblies RNA fragments into geometrically plausible models that meet user-provided secondary structure constraints, restraints on tertiary contacts and Small Angle X-ray Scattering data. We illustrate the method description with detailed benchmarks and its application to structural studies of viral RNAs with SAXS restraints.</p>
RNA 3D structural models used to train, test and validate lociPARSE
<p>This repository contains all the training, validation and test decoy sets to train and evalaute lociPARSE. It also contains training and benchmarks set-2 decoys from ARES.</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>
3dRNA/DNA: 3D Structure Prediction from RNA to DNA
Open the record for dataset details and reuse information.
ATAC-seq and RNA-seq for MDCKII 3D and 2D epithelial morphogenesis
GEO Series GSE129824. Canis lupus familiaris. 36 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [RNA-seq 1]
GEO Series GSE206362. Solanum lycopersicum. 6 samples. Type: Expression profiling by high throughput sequencing.
Dose-dependent sensitivity of human 3D chromatin to a heart disease-linked transcription factor [RNA-Seq]
GEO Series GSE285277. Homo sapiens. 42 samples. Type: Expression profiling by high throughput sequencing.
Super Pol II Domains enhance minor ZGA through 3D-interaction to ensure the integrity of major transcriptional waves in ZGA delayed mammals (RNA-Seq)
GEO Series GSE264468. Bos taurus; Bos grunniens x Bos taurus. 48 samples. Type: Expression profiling by high throughput sequencing.
Enhanced Media Optimize Bovine Myogenesis in 2D and 3D Models for Cultivated Meat Applications [RNA-Seq]
GEO Series GSE262675. Bos taurus. 15 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq: Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci
GEO Series GSE54952. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
RNA-sequencing of endothelial cells and 3D cardiac microtissues from hiPSCs
GEO Series GSE151427. Homo sapiens. 31 samples. Type: Expression profiling by high throughput sequencing.
Integrated analyses highlight interactions between the 3D-genome and DNA, RNA, and epigenomic alterations in metastatic prostate cancer
GEO Series GSE249494. Homo sapiens. 80 samples. Type: Other.
Bi-directional Impacts of Heterotypic Interactions in Engineered 3D Human Cardiac Microtissues Revealed by Single-Cell RNA-Sequencing and Functional Analysis
GEO Series GSE155226. Homo sapiens. 11 samples. Type: Expression profiling by high throughput sequencing.
THE EPIGENOME PLAYS A MAJOR ROLE IN TOMATO 3D CHROMATIN ORGANIZATION [RNA-seq]
GEO Series GSE243910. Solanum lycopersicum. 4 samples. Type: Expression profiling by high throughput sequencing.
Single-cell 3D genome structure reveals distinct human pluripotent states (RNA-Seq)
GEO Series GSE260994. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
RNA-sequencing of D2A1 and D2.OR cell lines in both 2D and 3D cultures
GEO Series GSE172882. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Establishment of 3D chromatin structure after fertilization and the metabolic switch at the morula-to-blastocyst transition require CTCF [RNA-seq]
GEO Series GSE180306. Mus musculus. 28 samples. Type: Expression profiling by high throughput sequencing.
Modelling human pre-gastulation development by 3D culture of blastoids generated from the primed-to-naive transitioning intermediates [RNA-seq]
GEO Series GSE200933. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Transcription and loop extrusion cooperatively shape the 3D genome of developing slime mold Dictyostelium discoideum [RNA-seq]
GEO Series GSE246367. Dictyostelium discoideum. 8 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.