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Dataset results
88 results for “granuloma”
scRNA-seq data for article: Kupffer cell and recruited macrophage heterogeneity orchestrate granuloma maturation and hepatic immunity in visceral leishmaniasis
<p>Single-cell RNA-seq dataset from sorted CD11bInt, F4/80Hi, CD64+ mouse liver cells in naive or Leishmania infantum-infected animals at 42 d.p.i.. Data analyses and results are described in manuscript: "Kupffer cell and recruited macrophage heterogeneity orchestrate granuloma maturation and hepatic immunity in visceral leishmaniasis". Data files are Seurat objects in RDS format. Filtered-out potential doublets, low quality cells and dying cells (excluded cells with <1000 genes detected, cells with >6000 genes detected, cells with mitochondrial gene expression > 10% and cells with <5000 transcript molecules). Data normalization, scaling and integration performed using Seurat.</p> <p>Filtered dataset containing all KCs and macrophages is in the "pessenda_KC_Macro_seurat" file.</p> <p>Our data were then mapped onto a reference dataset published by Remmerie et al. (DOI: 10.1016/j.immuni.2020.08.004) for annotation consistent with the literature. The reference mapped object can be found in the "pessenda_refmap_KC_Macro_seurat" file.</p> <p>Dataset containing the additional analysis of CLEC4F-TIM4+ FACS-sorted KCs can be found in the "pessenda_refmap_KCTimPos_seurat" file.</p>
Immunohistochemistry of Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control
<p>(A) Architecture of macaque TB lung granuloma, where lymphocytes and macrophages are present in distinct regions. Immunohistochemistry and confocal microscopy were performed on a granuloma from an animal at 11 weeks post-Mtb infection to visualize localization of CD11c+ macrophages (cyan), CD3+ T cells (yellow), and CD20+ B cells (magenta)</p> <p>(B) Detection of mast cells in a 10-week NHP granuloma using immunohistochemistry, staining for tryptase (green) and c-kit (CD117)(red).</p> <p>(C) Detection of mast cells in a human lung granuloma. Hematoxylin and eosin stain and immunohistochemistry with multinucleated giant cells (stars, (top left) and c-kit (CD117) staining (indicated by arrows, top and bottom right).</p>
Single-cell profiling identifies ACE+ granuloma macrophages as a non-permissive niche for intracellular bacteria during persistent Salmonella infection
<p>Macrophages mediate key antimicrobial responses against intracellular bacterial pathogens, such as <em>Salmonella enterica</em>. Yet, they can also act as a permissive niche for these pathogens to persist in infected tissues within granulomas, which are immunological structures comprised of macrophages and other immune cells. We apply single-cell transcriptomics to investigate macrophage functional diversity during persistent <em>Salmonella</em> <em>enterica</em> serovar Typhimurium (<em>S</em>Tm) infection in mice. We identify determinants of macrophage heterogeneity in infected spleens and describe populations of distinct phenotypes, functional programming, and spatial localization. Using a <em>S</em>Tm mutant with impaired ability to polarize macrophage phenotypes, we find that angiotensin converting enzyme (ACE) defines a granuloma macrophage population that is non-permissive for intracellular bacteria and their abundance anticorrelates with tissue bacterial burden. Disruption of pathogen control by neutralizing TNF is linked to preferential depletion of ACE<sup>+</sup> macrophages in infected tissues. Thus ACE<em><sup>+</sup></em> macrophages have limited capacity to serve as cellular niche for intracellular bacteria to establish persistent infection.</p>
Single-cell profiling identifies ACE+ granuloma macrophages as a non-permissive niche for intracellular bacteria during persistent Salmonella infection
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Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma - Location Data
<p>This dataset is meant to be used with "Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma - Results and Data". It provides spatial output data for 4 different setups (spheroid, traditional, 3d gravity, and traditional floating) of an agent-based model of <i>in vitro </i>tuberculosis infection models. </p>
CD4+ T cells re-wire granuloma cellularity and regulatory networks, promoting immunomodulation following Mtb reinfection
<p>Here we include the necessary .ipynb, .h5ad, and .rds (used for cell-cell interaction analyses) files used in our work: "Immunomodulatory re-wiring of granuloma cellularity and regulatory networks by CD4 T cells following Mtb reinfection"</p>
Treatment of Tracheostomy Granulomas
ClinicalTrials.gov study NCT02116608. IPD Sharing: NO. Countries: 1. Publications: 4.
Histological and TEM data: A major ecological niche of eosinophils in evolving Schistosoma granulomas challenges the eosinophil view as “helminth killer” cells
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Spatial transcriptomics of an innate granuloma in a mouse infection model with Chromobacterium violaceum
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Single-cell and spatial transcriptomics reveal aberrant lymphoid developmental programs driving granuloma formation
<p>Raw microscopy images underlying the publication "Single-cell and spatial transcriptomics reveal aberrant lymphoid developmental programs driving granuloma formation"</p>
TB and Sarcoidosis Granuloma
ClinicalTrials.gov study NCT06396910. IPD Sharing: NO. Countries: 1. Publications: 1.
Granuloma Annulare Treated With Rifampin, Ofloxacin, and Minocycline Combination Therapy
ClinicalTrials.gov study NCT00720980. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Open-label Trial of Tofacitinib in Cutaneous Sarcoidosis and Granuloma Annulare
ClinicalTrials.gov study NCT03910543. IPD Sharing: NO. Countries: 1. Publications: 3.
Treatment of Granuloma Umbilical in Newborn Babies
ClinicalTrials.gov study NCT01567215. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Efficacy Study of Botulinum Toxin (BOTOX) Injections to Treat Vocal Fold Granulomas
ClinicalTrials.gov study NCT01678053. IPD Sharing: Not stated. Countries: 1. Publications: 6.
Expression and Role of the JAK/STAT Pathway in Sarcoidosis Granuloma Cells
ClinicalTrials.gov study NCT04751279. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Fluorescent in situ hybridization of Mycobacterium tuberculosis rRNA species for analysis of ribosomal synthesis as a marker of bacterial growth of individual bacilli in distinct lesional microenvironments of lung granulomas from C3HeB/FeJ mice
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Differential transcriptomics in sarcoidosis lung and lymph node granulomas with comparisons to pathogen-specific granulomas
GEO Series GSE157671. Homo sapiens. 31 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide characterization of a novel necrotic granuloma model of latent tuberculosis infection and reactivation in mice
GEO Series GSE55183. Mus musculus. 4 samples. Type: Expression profiling by array.
Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets II
GEO Series GSE174566. Homo sapiens. 36 samples. Type: Expression profiling by high throughput sequencing.
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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.