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60 results for “Tertiary Structure”
Progress Toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure
<p>Supplementary repository for the "Progress Toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure" article. Contains the simulation on the <em>Didymium iridis</em> lariat-capping ribozyme (DiLCrz, PDB ID: 4P8Z).</p>
Improving AlphaFold2-based Protein Tertiary Structure Prediction with MULTICOM in CASP15
<p>Improving AlphaFold2-based Protein Tertiary Structure Prediction with MULTICOM in CASP15</p>
Dataset related to article "NK cell recruitment in salivary glands provides early viral control but is dispensable for tertiary lymphoid structure formation."
<p>Salivary glands (SGs) represent a permissive site for several sialotropic viruses whose persistence is linked to the development of autoimmunity. Natural Killer (NK) cells play a key role in viral clearance but their involvement in viral infection control and in tertiary lymphoid structures (TLS) development within SGs is unknown. By using an inducible model of TLS in the SGs of wild-type C57BL/6 mice, induced by the local delivery of a replication-defective adenovirus (AdV), we demonstrated that circulating NK cells are rapidly recruited to SGs and highly enrich the early inflammatory infiltrate prior to TLS development. NK cells migrating to SGs in response to AdV infection up-regulate NKp46, undergo proliferation, acquire cytotoxic potential, produce Granzyme-B and IFN-γ, and reduce viral load in the acute phase of the infection. Nonetheless, the selective depletion of both circulating and infiltrating NK cells in AdV-infected mice neither affect the development and frequency of TLS nor the onset of autoimmunity. These data demonstrate that, upon local viral delivery of AdV, peripheral NK cells homing to SGs can exert an early control of the viral infection but are dispensable for the formation of TLS and breach of immunologic tolerance.</p> <p> </p> <p>This research used pzf and ets file form extensions, we attach pdfs information about</p>
Dataset for "A Comparative Review of Deep Learning Methods for RNA Tertiary Structure Prediction"
<p>Datasets used in "A Comparative Review of Deep Learning Methods for RNA Tertiary Structure Prediction".</p> <p>The provided zip file contains:</p> <ul> <li><strong>Datasets 1–3:</strong> For each dataset, directories include input sequences (FASTA), multiple sequence alignments (MSAs in AFA format), and normalized predicted structures from six deep learning tools. Dataset 3 also contains references - RNA chains extracted from complexes. These folders also include a CSV file with all metrics for all RNAs and tools.</li> <li><strong>Dataset 4:</strong> A text file listing the PDB IDs of RNAs included in this dataset, which is a subset of Dataset 3.</li> <li><strong>Dataset complexes:</strong> RNA chains extracted from predicted complexes, where predictions are made by AlphaFold 3 web server and, in some cases, RoseTTAFoldNA. There are also job files for the AlphaFold 3 web server used to obtain these predictions. Same as for previous datasets, this folder also includes a CSV file with all metrics for these RNA chains.</li> </ul> <p>The structure of the dataset and details of each folder are explained in the included README file.</p> <p> </p>
FASST Structure Database files for "Tertiary motifs as building blocks for the design of protein-binding peptides"
<p>FASST Database files for use in the <a href="https://github.com/swanss/peptide_design">peptide design</a> pipeline.</p> <p>A complete list of structures provided in the databases is provided in the supplementary information of the Protein Science article.</p> <p>Singlechain structures: <a href="https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fpro.4322&file=pro4322-sup-0004-TableS6.txt">pro4322-sup-0004-TableS6.txt</a> (format: PDBID_CHAINID)</p> <p>Multichain structures: <a href="https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fpro.4322&file=pro4322-sup-0005-TableS7.txt">pro4322-sup-0005-TableS7.txt</a> (format: PDBID)</p>
Spatial dynamics of CD39⁺CD8⁺ exhausted T cells reveal tertiary lymphoid structures-mediated response to PD-1 blockade in esophageal cancer
<p><strong>Data related to the paper</strong>: <em>"Spatial dynamics of CD39+CD8+ exhausted T cells reveal tertiary lymphoid structures-mediated response to PD-1 blockade in esophageal cancer,”</em> <em>Nature Communications</em> (2024)</p> <p>The repository data consists of two main folders: <strong>IMC_dataset</strong> and <strong>MC_normalized_dataset</strong>.</p> <p><strong>IMC_dataset</strong> includes:</p> <ol> <li> <p><strong>IMC_denoised_dataset</strong>: This folder contains cell mask images and noise-reduced images for each sample.</p> </li> <li> <p><strong>IMC_raw_dataset</strong>: This folder contains raw, unprocessed data.</p> </li> <li> <p><strong>IMC_processed_data</strong>: This folder contains standardized single-cell information and spillover-corrected FCS files, along with the compensation matrix.</p> </li> </ol> <p>The <strong>MC_normalized dataset</strong> includes FCS files that have been sorted by barcode.</p> <p><strong>Please note</strong> that in the IMC dataset, the following mass channels are blank:</p> <ul> <li><strong>Tumor-ROI</strong>: 80Ar, 127I, 131Xe, 145Nd, 146Nd, 149Sm, 160Gd, 171Yb, 174Yb, 176Yb, 190Os</li> <li><strong>SLO-ROI</strong>: 80Ar, 127I, 131Xe, 145Nd, 146Nd, 149Sm, 160Gd, 176Yb, 190Os</li> </ul> <p>The names attached to the file names are IDs.</p>
Immunotherapy response induces divergent tertiary lymphoid structure morphologies in hepatocellular carcinoma
<p>This repository contains imaging mass cytometry (IMC) data and associated files for the publication "Immunotherapy response induces divergent tertiary lymphoid structure morphologies in hepatocellular carcinoma". Code used to analyze these data can be found at https://github.com/FertigLab/HCCTLS. Raw IMC data have been uploaded as .mcd files (n=10). The file "IMCpanel.xlsx" indicates the antibodies used for each IMC channel. In addition, we have uploaded .tiff files (n=38) generated from each .mcd, which were used to identify and annotate individual tertiary lymphoid structures (TLS) as some ROI had multiple TLS. The file "Updated Catalogue of TLS with S numbers.xlsx" indicates which TLS correspond to each ROI in the .mcd files. To determine the area of each TLS, .tiff files were annotated using ImageJ and the area of each TLS was exported and stored in the file, "TLS_selection_area_pixels.csv". The XY coordinates of individual TLS were obtained by using FlowJo software to annotate .fcs files resulting from single cell segmentation of each ROI. </p>
Presence of tertiary lymphoid structures and exhausted tissue-resident T cells determines clinical response to PD-1 blockade in renal cell carcinoma
Open the record for dataset details and reuse information.
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>
Molecular and spatial analysis unveils the functional basis of tertiary lymphoid structures in Sjogren’s syndrome[bulk RNA-seq]
GEO Series GSE272410. Homo sapiens. 73 samples. Type: Expression profiling by high throughput sequencing.
Trigger inducible tertiary lymphoid structure formation using covalent organic frameworks for cancer immunotherapy
GEO Series GSE268619. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Choroid plexus tertiary lymphoid structures in lupus: a novel neuro-immune interface
GEO Series GSE99030. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade [scRNA-seq]
GEO Series GSE272347. Homo sapiens. 17 samples. Type: Expression profiling by high throughput sequencing; Other.
Novel Immunotherapy-Induced Tertiary Lymphoid Aggregates Accumulate as Intratumoral Nodal Structures of Immune Regulation in Pancreatic Cancer
GEO Series GSE52171. Homo sapiens. 20 samples. Type: Expression profiling by array.
Gut-Resident IL10+CX3CR1hi Macrophages Induce Tertiary Lymphoid Structures and IgA Response in Situ
GEO Series GSE121471. Mus musculus. 69 samples. Type: Expression profiling by high throughput sequencing.
Molecular and spatial analysis unveils the functional basis of tertiary lymphoid structures in Sjogren’s syndrome[scRNA-seq]
GEO Series GSE272409. Homo sapiens. 13 samples. Type: Expression profiling by high throughput sequencing.
Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer
GEO Series GSE175540. Homo sapiens. 24 samples. Type: Expression profiling by high throughput sequencing.
RNA tertiary structure and conformational dynamics revealed by BASH MaP
GEO Series GSE271825. synthetic construct; Homo sapiens. 26 samples. Type: Other.
Fc-optimized CD40 Agonistic Antibody Induces Tertiary Lymphoid Structures and Systemic Antitumor Immunity in Metastatic Cancer Patients [Human]
GEO Series GSE298047. Homo sapiens. 48 samples. Type: Other; Expression profiling by high throughput sequencing.
Spatial immune profiling defines a subset of human gliomas with functional tertiary lymphoid structures [Xenium]
GEO Series GSE302502. Homo sapiens. 12 samples. Type: Other.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.