Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
134
datasets available to search
ShareScore release 0.9.0
Dataset results
134 results for “Tonsils”
Highly multiplexed histology reveals phenotypic and spatial characteristics of human Innate Lymphoid Cells in chronic inflammation - MELC tonsil data-set
<p><strong>53 marker MELC Run in human tonsil</strong>. Each image depicts the same field of view, sequentially stained with the depicted fluorescence-labelled antibodies. Images contain 2048 x 2048 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have not been normalized and intensities have not been adjusted.</p> <p> </p>
Tonsil Atlas: CellRanger outputs
<p>This repository contains all the expression and accessibility matrices for each of the five data modalities (scRNA-seq, scATAC-seq, Multiome, CITE-seq+scVDJ-seq, and spatial transcriptomics) associated with the article "An Atlas of Cells in The Human Tonsil," published in Immunity in 2024. In particular, each modality was produced with different platforms from 10X Genomics and processed with different versions of CellRanger. This repository contains the most important outputs from each CellRanger run of each library. In addition, it also includes de expression and accessiblity matrices for the two mantle cell lymphoma (MCL) patients analyzed in the paper.</p> <p>Version 4.0 of this repository adds all high-quality TIFF images of the Visium slides, as requested by a user.</p>
OMAP-10: Multiplexed Antibody-Based Imaging of Human Palatine Tonsil with MACSima v1.0
<p> </p> <p>OMAP-10 was designed for MACSima (MACSima imaging cyclic staining) imaging of <em>paraformaldehyde</em> (PFA)-fixed human tonsil samples. The MACSima technology is described in detail in the following publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">https://doi.org/10.1038/s41598-022-05841-4</a>). Most, but not all, antibodies in this panel are recombinant antibodies with a mutated human IgG1 constant region. The described mutation removes the Fc receptor binding capacity of human IgG1, eliminating the need for additional blocking steps and reducing non-specific binding of human antibodies on human tissues. Highly multiplexed imaging is achieved through cycles of immunolabeling with FITC, PE, and APC conjugated antibodies and photobleaching to eliminate fluorescence signal between imaging cycles. The panel contains 30 antibodies and the nuclear marker DAPI for image alignment and nuclear segmentation. This OMAP provides a spatial context for all anatomical structures and most cell types present in the ASCT+B tonsil table, v1.0 (submitted for review). OMAP-10 follows closely OMAP-1 described for human lymph nodes (<a href="https://hubmapconsortium.github.io/ccf-releases/v1.3/docs/omap/omap-1-human-lymph-node-ibex.html">https://hubmapconsortium.github.io/ccf-releases/v1.3/docs/omap/omap-1-human-lymph-node-ibex.html</a>). The initial dataset associated with OMAP-10 can be found in this dataset. All reagents were obtained from Miltenyi Biotec and have been rigorously tested through an internal quality control system to have minimal variation between lots. For this reason, lot information is not included in the table below. Analysis was performed by an accompanied software package MACSIQ View Analysis also described in the MACSima publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">https://doi.org/10.1038/s41598-022-05841-4</a>). The plan was to also include the data analysis in the uploaded dataset. However mixing the original data with analyses data would lead to confusion. Therefore only the original image files are included here. This is in brief the image analysis pipeline: the software processes the raw images of the MACSima run, generates stitched images, and then allows downstream analysis including cell segmentation, cell gating, data normalization, dimension reduction plots (tSNE, UMAP), heat maps, distance analyses and cluster analyses, all of which are interactively linked together. The MACSima system is continuously evolving, and this is the first OMAP dataset generated by using the MACSima system (Instrument, Reagents and Software).</p> <p>The images enclosed are in OME-tif format (16 bit depth). The optical resolution is 0.17 micron/pixel. The imaged area size is 1.6 mm x 1.3 mm. This Data is currently under review by the OMAP community and changes are still possible in the follow up version. The image contains stichted images of 9 fields of view. The complete runtime on the MACSima for this image dataset was about 12 hours on the instrument. The OMAP description also links to the ASCT+B table for the palatine tonsil.</p> <p><strong>Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Palatine Tonsil v1.0</strong></p> <p><strong>Description</strong></p> <p><a href="https://hubmapconsortium.github.io/ccf/pages/ccf-anatomical-structures.html">Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables</a> aim to capture the nested <em>part of</em> structure of anatomical human body parts, the typology of cells, and biomarkers used to identify cell types. The tables are authored and reviewed by an international team of experts. The Palatine Tonsil ASCT+B table is derived from published literature, public datasets, and unpublished studies from table authors. The Palatine Tonsil is part of the tonsiluar ring of Waldeyer network. In comparison to other Tonsils the Palatine Tonsil has an enlarged lymphoid tissue.</p> <p>The gene biomarkers are primarily derived from a preprint on an Atlas of Cells of the human tonsil (<a href="https://www.biorxiv.org/content/10.1101/2022.06.24.497299v1">Ramon Massoni-Badosa et al 2022</a>). The tonsil azimuth data set can be explored <a href="https://azimuth.hubmapconsortium.org/references/human_tonsil/">here</a> .Cell phenotypes, especially for antibody-based assays like the MACSima are very complex and in its first version, only the basic cell types are listed with many more to be included in the next iteration of the ASCT+B table. The correlation between protein detection and RNA expression data at the single cell level needs to be established. In total, this table reports 13 anatomical structures, 17 cell types, and 30 biomarkers. </p> <p>The following list contains the file name and the target name of the antibody used in a given staining:</p> <p>ACTIN_REAL650/ACTA2</p> <p>Bcl2_REA872/BCL2</p> <p>CD11c_REAL235/ITGAX</p> <p>CD138_REA929/SDC1</p> <p>CD15_VIMC6/FUT4</p> <p>CD19_REAL106/CD19</p> <p>CD1c_REA694/CD1C</p> <p>CD209_REAL1087/CD209</p> <p>CD20_REA1087/MS4A1</p> <p>CD21_REA940/CR2</p> <p>CD274_PDL1/CD274</p> <p>CD279_REAL531/PDCD1</p> <p>CD27_REA499/CD27</p> <p>CD39_REA739/ENTPD1</p> <p>CD3_REAL1097/CD3E</p> <p>CD44_REA690/CD44</p> <p>CD4_REA1307/CD4</p> <p>CD68_REA1306/CD68</p> <p>CD79a_REA1142/CD79A</p> <p>CD8_REA734/CD8A</p> <p>CollagenIV_REAL1212/COL4A1</p> <p>Cytokeratin_CK36H5/KRT7,KRT8,KRT18,KRT19</p> <p>FoxP3_REA1253/FOXP3</p> <p>HLADR_REAL550/HLA-DRA</p> <p>IgD_REA740/IGHD</p> <p>IgM_REAL689/IGHM</p> <p>Ki67_REA183/MKI67</p> <p>PlasmaCell_REA908/CKAP4</p> <p>Vimentin_REA409/VIM</p>
OMAP-21: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Palatine Tonsil with MICS on MACSima 1.5
<p>OMAP-21 was designed for MICS (MACSima imaging cyclic staining) imaging of FFPE human tonsil samples. Tissue fixation and antigen retrieval is described in (<a href="https://www.biorxiv.org/content/biorxiv/early/2023/11/07/2023.10.27.564191.full.pdf">Spatial protein and RNA analysis on the same tissue section using MICS technology</a>). The MACSima technology is described in detail in the following publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">MACSima imaging cyclic staining (MICS) technology reveals combinatorial target pairs for CAR T cell treatment of solid tumors</a>). Most, but not all, antibodies in this panel are recombinant antibodies with a mutated human IgG1 constant region. The described mutation removes the Fc receptor binding capacity of human IgG1, eliminating the need for additional blocking steps and reducing non-specific binding of human antibodies on human tissues. Highly multiplexed imaging is achieved through cycles of immunolabeling with FITC, PE, and APC conjugated antibodies and photobleaching to eliminate fluorescence signal between imaging cycles. The panel contains 47 antibodies and the nuclear marker DAPI for image alignment and nuclear segmentation. This OMAP provides a spatial context for all anatomical structures and most cell types present in the human palatine tonsil. OMAP-21 follows closely OMAP-1 described for human lymph nodes (<a href="https://cdn.humanatlas.io/hra-releases/v1.4/docs/omap/omap-1-human-lymph-node-ibex.html">omap-1-human-lymph-node-ibex</a>) and OMAP-10 (<a href="https://cdn.humanatlas.io/hra-releases/v1.4/docs/omap/omap-10-palatine-tonsil-macsima.html">omap-10-palatine-tonsil-macsima</a>).</p> <p>All reagents were obtained from Miltenyi Biotec and have been rigorously tested through an internal quality control system to have minimal variation between lots. For this reason, lot information is not included in this table. Analysis was performed by an accompanied software package MACSIQ View Analysis also described in the MACSima publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">https://doi.org/10.1038/s41598-022-05841-4</a>). The result of the analysis is included in the uploaded dataset. In brief, the software processes the raw images of the MACSima run, generates stitched images, and then allows downstream analysis including cell segmentation, cell gating, data normalization, dimension reduction plots (tSNE, UMAP), heat maps, distance analyses and cluster analyses, all of which are interactively linked together. The MACSima system is continuously evolving, this is the second OMAP for the MACSima system. A representative dataset created using OMAP-21 can be found here:<a href="https://doi.org/10.5281/zenodo.7875937"> </a><strong> 10.5281/zenodo.11281609 .</strong></p>
Pharmacodynamic Effects of Ribavirin in Patients With Tonsil and/or Base of Tongue Squamous Cell Carcinoma
ClinicalTrials.gov study NCT01268579. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Tonsil Surgery in Recurrent or Chronic Tonsillitis
ClinicalTrials.gov study NCT04657549. IPD Sharing: YES. Countries: 1. Publications: 3.
OMAP-19 Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Tonsil with IBEX
<p>Representative dataset acquired using the Iterative Bleaching Extends multi-pleXity (IBEX) imaging method described in:</p> <ol> <li>“IBEX: A versatile multi-plex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues“, A. Radtke et al., <em>Proc. Natl. Acad. Sci. USA,</em> 2020, <a href="https://doi.org/10.1073/pnas.2018488117">doi.org/10.1073/pnas.2018488117</a>.</li> <li>"IBEX: an iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues", A. J. Radtke, et al., <em>Nat Protoc</em>, 2022, <a href="https://doi.org/10.1038/s41596-021-00644-9">doi.org/10.1038/s41596-021-00644-9</a>.</li> </ol> <p>This dataset accompanies the <a href="https://www.nature.com/articles/s41592-023-01846-7">Organ Mapping Antibody Panel (OMAP) effort</a> led by the <a href="https://commonfund.nih.gov/HuBMAP">Human BioMolecular Atlas Program</a> detailed <a href="https://humanatlas.io/omap">here</a>.</p> <p>OMAP-19 was designed for IBEX imaging of human FFPE tonsil samples sectioned onto glass slides. The panel consists of 6 cycles of 20 primary antibodies, 5 secondary antibodies, and the nuclear label Hoechst for image alignment and nuclear segmentation. This OMAP provides a spatial context for 10 anatomical structures and at least 16 cell types present in the <a href="https://cdn.humanatlas.io/hra-releases/v2.0/docs/asct-b/asct-b-vh-palatine-tonsil.copy.html">ASCT+B tonsil table</a>. OMAP-19 was designed to examine myeloid subsets (CD11b, CD11c, CD14, CD15, HLA-DR) and angiogenesis (VEGF-A and VEGF-C) in human ovarian cancer biopsies. The human tonsil was used as a positive control for antibody validation and panel development. Antigen retrieval was performed using a pressure cooker (Borg Decloaker BD1000, 110°C for 15 minutes) and a tris-based buffer (pH 9.5). Several custom antibodies were created using commercial labeling kits as indicated in the associated RRID entries for these antibodies. More details on the antigen retrieval protocol and step-by-step application of antibodies can be found on the <a href="https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/">IBEX Imaging Community knowlege-base</a> (current version) and on <a href="../records/7693279">Zenodo</a> (last official version).</p> <p>Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as a 405 nm laser. All images were captured at an 16-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.379 µm), y (0.379 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software.</p> <p>Image supplied as a .ims Imaris Format file and can be opened with the <strong>free</strong> <a href="https://imaris.oxinst.com/imaris-viewer">Imaris Viewer</a> software or <a href="https://imagej.net/software/fiji/">ImageJ/Fiji</a>. Image channel and antibody meta-data supplied as an xlsx file.</p>
Seurat objects associated with the tonsil cell atlas
<p>In the context of the Human Cell Atlas, we have created a single-cell-driven taxonomy of cell types and states in human tonsils. This repository contains the Seurat objects derived from this effort. In particular, we have datasets for each modality (scRNA-seq, scATAC-seq, CITE-seq, spatial transcriptomics), as well as cell type-specific datasets. Most importantly, this is the input that we used to create the HCATonsilData package, which allows programmatic access to all this datasets within R.</p> <p>Version 2 of this repository includes cells from 7 additional donors, which we used as a validation cohort to validate the cell types and states defined in the atlas. In addition, in this version we also provide the Seurat object associated with the spatial transcriptomics data (10X Visium), as well as the fragments files for scATAC-seq and Multiome</p>
Dexlansoprazole to Treat Laryngopharyngeal Reflux and Lingual Tonsil Hypertrophy
ClinicalTrials.gov study NCT01328652. IPD Sharing: Not stated. Countries: 1. Publications: 12.
Microbiology of Severe Acute Tonsillitis, Peritonsillar Cellulitis, and Infectious Mononucleosis
ClinicalTrials.gov study NCT02715037. IPD Sharing: NO. Countries: 1. Publications: 4.
Tonsillectomy in Recurrent Tonsillitis
ClinicalTrials.gov study NCT00136877. IPD Sharing: Not stated. Countries: 1. Publications: 1.
L. Reuteri ATCC PTA 5289 & L. Reuteri DSM 17938 for the Treatment of Children With Pharyngitis and/or Tonsillitis
ClinicalTrials.gov study NCT03377374. IPD Sharing: NO. Countries: 1. Publications: 5.
Children Recovering From Tonsil Surgery
ClinicalTrials.gov study NCT03292068. IPD Sharing: NO. Countries: 1. Publications: 11.
Efficacy of a Nurse Telephone Follow-up on Pain Intensity After Removal of Tonsils in Children
ClinicalTrials.gov study NCT01568372. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Evaluating the Genetics and Immunology of Periodic Fever, Aphthous Stomatitis, Pharyngitis, and Cervical Adenitis (PFAPA) Syndrome and Other Tonsil Disorders
ClinicalTrials.gov study NCT05656365. IPD Sharing: YES. Countries: 1. Publications: 3.
Intravenous Lidocaine in the Prevention of Postoperative Vomiting in Elective Tonsil Surgery
ClinicalTrials.gov study NCT01986309. IPD Sharing: Not stated. Countries: 1. Publications: 1.
the Effectiveness of Lactoferrin in Treatment of Iron Deficiency Anemia in Children With Chronic Tonsillitis
ClinicalTrials.gov study NCT03748043. IPD Sharing: NO. Countries: 1. Publications: 2.
Study of Imupret Application in the Technology of Delayed Prescription of Antibiotics in Patients With Acute Tonsillitis
ClinicalTrials.gov study NCT04537819. IPD Sharing: NO. Countries: 1. Publications: 1.
Effects of Propofol on Respiratory Adverse Events During Extubation in Children Undergoing Tonsil Adenoidectomy
ClinicalTrials.gov study NCT05769842. IPD Sharing: NO. Countries: 1. Publications: 4.
Complication Registry for Tonsil Surgery
ClinicalTrials.gov study NCT02049372. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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.