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.
2,955
datasets available to search
ShareScore release 0.9.0
Dataset results
2,955 results for “immune response”
Data from: Comparison of spleen transcriptomes of two wild rodent species reveals differences in the immune response against Borrelia afzelii
<p>Different host species often differ considerably in susceptibility to a given pathogen, but the causes of such differences are rarely known. The natural hosts of the tick-transmitted bacterium <i>Borrelia afzelii</i>, which is one of causative agents of Lyme borreliosis in humans, include a variety of small mammals like voles and mice. Previous studies have shown that <i>B. afzelii-</i>infected bank voles (<i>Myodes glareolus</i>) have about ten times higher bacterial load than infected yellow-necked mice (<i>Apodemus flavicollis</i>), indicating that these two species differ in resistance. In this study, we compared the immune response to <i>B. afzelii </i>infection in these host species by using RNA-sequencing to quantify gene expression in spleen. Gene set enrichment analysis (GSEA) showed that several immune pathways were down-regulated in infected animals in both bank voles and yellow-necked mice. Moreover, IFNα response was up-regulated in <i>B. afzelii</i>-infected yellow-necked mice, while IL6 signaling and the complement pathway were down-regulated in infected bank voles; differences in regulation of these three pathways between bank voles and yellow-necked mice could thus contribute to the difference in resistance to <i>B. afzelii</i> between the species. This study provides knowledge of gene expression induced by a zoonotic pathogen in its natural host, and possible species-specific regulation of immune responses associated with resistance.</p>
Gene expression remodelling and immune response during adaptive divergence in an African cichlid fish
<p><span>Variation in gene expression contributes to ecological speciation by facilitating population persistence in novel environments. Likewise, immune response can be a relevant factor in speciation driven by adaptation to different environments. Previous studies examining gene expression differences between recently diverged ecotypes often relied on only one pair of populations, targeted the expression of only a subset of genes, or used wild caught-individuals. Here, we investigated the contribution of habitat-specific parasites and symbionts and the underlying immunological capabilities of ecotype hosts to adaptive divergence in lake-river population pairs of the cichlid fish <i>Astatotilapia burtoni</i>. To shed light on the role of phenotypic plasticity in adaptive divergence, we compared parasite and microbiota communities, immune response, and gene expression patterns of fish from natural habitats and a lake-like pond setup. In all investigated population pairs, lake fish were more heavily parasitized than river fish, both in terms of parasite taxa composition and infection abundance. Innate immune response in the wild was higher in lake than in river populations and elevated in a river population exposed to lake parasites in the pond setup. Environmental differences between lake and river habitat and their distinct parasite communities shaped differential gene expression, involving genes functioning in osmoregulation and immune response. Most changes in gene expression between lake and river samples in the wild and in the pond setup were based on a plastic response. Finally, gene expression and bacterial communities of wild-caught individuals and individuals acclimated to lake-like pond conditions showed shifts underlying adaptive phenotypic plasticity.</span></p>
Prior exposure to long day photoperiods alters immune responses and increases susceptibility to parasitic infection in stickleback
<p>Seasonal disease and parasitic infection are common across organisms, including humans, and there is increasing evidence for intrinsic seasonal variation in immune systems. Changes are orchestrated through organisms' physiological clocks using cues such as day length. Ample research in diverse taxa has demonstrated multiple immune responses are modulated by photoperiod, but to date, there have been few experimental demonstrations that photoperiod cues alter susceptibility to infection. We investigated the interactions among photoperiod history, immunity, and susceptibility in laboratory-bred three-spined stickleback, a long-day breeding fish, and its external, directly-reproducing, monogenean parasite <i>Gyrodactylus gasterostei</i>. We demonstrate that previous exposure to long day photoperiods (PLD) increases susceptibility to infection relative to previous exposure to short days (PSD), and modifies the response to infection for the mucin gene <i>muc2</i> and Treg cytokine <i>foxp3a</i> in skin tissues in an intermediate 12L:12D photoperiod experimental trial. Expression of skin <i>muc2</i> is reduced in PLD fish, and negatively associated with parasite abundance. We also observe inflammatory gene expression variation associated with natural inter-population variation in resistance, but find that photoperiod modulation of susceptibility is consistent across host populations. Thus, photoperiod-modulation of the response to infection is important for host susceptibility, highlighting new mechanisms affecting seasonality of host-parasite interactions.</p>
Data from: Anthelmintic drugs modulate the acute phase immune response but not the microbiota in wild Song Sparrows
<p>Co-infection with microparasites (e.g., bacteria) and macroparasites (e.g., helminths) is often the natural state for wild animals. Despite evidence that gut helminths can bias immune responses away from inflammatory processes, few field studies have examined the role that helminths, or their potential interactions with internal microbial communities, play in modulating immunity in free-living, wild birds. Here, we used anthelmintic drugs to treat wild Song Sparrows (<em>Melospiza melodia</em>) for helminth infections and measured markers of systemic inflammation (heterothermia and locomotor activity) in response to an immune challenge with lipopolysaccharide (LPS), a cell wall component of gram-negative bacteria. Using birds from a population that previously showed high helminth prevalence, we monitored skin temperature and activity remotely using automated radio telemetry. We also collected cloacal swabs to determine whether drug treatment was associated with changes in the cloacal microbiota, and whether cloacal microbial community structure was associated with the severity of birds' immune responses. Because helminths can reduce the severity of inflammatory immune responses in other species, we predicted that in comparison with untreated control birds, anthelmintic-treated birds would be more lethargic and display higher fevers when challenged with LPS. Consistent with these predictions, anthelmintic-treated birds expressed higher fevers in response to immune challenge. However, all LPS-challenged birds decreased locomotor activity to a similar degree, regardless of anthelmintic treatment. Although several individual indicator bacterial taxa were strongly associated with anthelmintic treatment, this treatment did not alter overall bacterial alpha- and beta- diversity. Similarly, we did not find evidence that bacterial community diversity influenced the severity of immune responses to LPS. These results suggest that under field conditions, natural helminth infection can reduce the severity of songbirds' thermoregulatory responses (fever) during an immune challenge, without major impacts on internal microbial communities or behavioral responses to infection.</p>
Characterization of the microbiome and immune response in corals with chronic Montipora white syndrome.
<p>Complete code and data files for the Motipora White Syndrome paper. Run in Qiime2 2020.11, mostly on the command line.</p>
PINK1 deficiency rewires early immune responses in a mouse model of Parkinson's disease triggered by intestinal infection
<p>Parkinson’s disease is characterized by a period of non-motor symptoms, including gastrointestinal dysfunction, preceding motor deficits by decades. This long prodrome is suggestive of peripheral immunity involvement in the initiation of disease. We previously developed a model system in PINK1 KO mice displaying PD-like motor symptoms at late stages following intestinal infections. Herein, we map the initiating immune events at the site of infection in this model. Using single-cell RNAseq, we demonstrate that peripheral myeloid cells are the earliest highly dysregulated immune cell type in PINK1 KO infected mice followed by an aberrant T cell response shortly after. We elucidate an increased propensity for antigen presentation mediated by myeloid-CD8+ T cell interaction. PINK1 KO activated myeloid cells acquire a proinflammatory profile inducing cytotoxic T cell responses. Together, our study provides the first evidence that PINK1 is a key regulator of immune functions in the gut underlying early PD-related disease mechanisms.</p>
Corticosterone and immune responses to dehydration in squamate reptiles
<p class="MsoListParagraph">Many environments present some degree of seasonal water limitations; organisms that live in such environments must be adapted to survive periods without permanent water access. Often this involves the ability to tolerate dehydration, which can have adverse physiological effects and is typically considered a physiological stressor. While having many functions, the hormone corticosterone (CORT) is often released in response to stressors, yet increasing plasma CORT while dehydrated could be considered maladaptive, especially for species that experience predictable bouts of dehydration and have related coping mechanisms. Elevating CORT could reduce immunocompetence and have other negative physiological effects. Thus, such species likely have CORT and immune responses adapted to experiencing seasonal droughts. We evaluated how dehydration affects CORT and immune function in eight squamate species that naturally experience varied water limitation.</p> <p class="MsoListParagraphCxSpLast">We tested whether hydric state affected plasma CORT concentrations and aspects of immunocompetence (lysis, agglutination, bacterial killing ability, and white blood cell counts) differently among species based on how seasonally water limited they are and whether this is constrained by phylogeny. The species represented four familial pairs, with one species of each pair inhabiting environments with frequent access to water and one naturally experiencing extended periods (>30 days) with no access to standing water.</p> <p class="MsoNormal">The effects of dehydration on CORT and immunity varied among species. Increases in CORT were generally not associated with reduced immunocompetence, indicating CORT and immunity might be decoupled in some species. Interspecies variations in responses to dehydration were more clearly grouped by phylogeny than habitat type.</p>
Genetic variants regulating the immune response improve the prediction of COVID-19 severity provided by clinical variables
<p>Data set generated to evaluate the association between SNPs from genes related to SARS-CoV-2 pathogenesis and their clinical outcome.</p>
Multiomics analyses reveal a Type III-associated immune response in immunotherapy-induced toxicity in melanoma and identifies potential new therapeutic targets
<p>Immune checkpoint inhibitors (ICIs) are standard-of-care for the treatment of advanced melanoma, but their use is limited by immune-related adverse events (irAEs). Proteomic analyses and multiplex cytokine/chemokine assays from serum at baseline and at irAEs onset in melanoma patients indicated aberrant T-cell activity with differential expression of Type I and III immune signatures. This was in line with an increase in the proportions of monocytes and decrease of IL-17A-producing CD4+ T-cells in the peripheral blood using single cell RNA sequencing. Multiplex immunohistochemistry and spatial transcriptomics on ICI-induced skin rash and colitis showed an increase in the proportion of CD4+ T-cells with IL-17A expression. </p> <p>Anti-IL-17A mAbs were administered in two patients with myocarditis, colitis and skin rash with resolution of the irAE. This study highlights the potential role of Type III CD4+ T-cells in irAEs development and provides proof-of-principle evidence for a corresponding clinical trial using anti-IL17A for treating irAEs.</p> <p>Code to generate the figures are located at https://github.com/pcheng84/AE_analysis/</p> <p> </p>
Multi-omics analysis of innate and adaptive responses to BCG vaccination reveals epigenetic cell states that predict trained immunity
<p>This repository contains personal immune profiles of 323 healthy individuals (300BCG) subjected to Bacillus Calmette-Guérin (BCG) with blood samples collected immediately before (day 0), and 14 and 90 days after the vaccination. The personal immune profiles comprise:</p> <ul> <li>immune cell concentrations measured with flow cytometry and a hematology analyzer</li> <li>plasma concentrations of 73 circulating inflammatory markers</li> <li>30 measurements of cytokine and lactate production capacity of peripheral blood mononuclear cells (PBMCs) in response to four microbial stimuli (Candida albicans, Escherichia coli lipopolysaccharide [LPS], Staphylococcus aureus, Mycobacterium tuberculosis).</li> </ul> <p>Visit <a href="http://300BCG.bocklab.org/">http://300BCG.bocklab.org/</a> to learn more.</p>
Leeches Baicalobdella torquata feed on hemolymph but have a low effect on the cellular immune response of amphipod Eulimnogammarus verrucosus from Lake Baikal
Open the record for dataset details and reuse information.
Population-level variation in parasite resistance due to differences in immune initiation and rate of response
<p>Closely related populations often differ in resistance to a given parasite, as measured by infection success or failure. Yet, the immunological mechanisms of these evolved differences are rarely specified. Does resistance evolve via changes to the host's ability to recognize that an infection exists, actuate an effective immune response, or attenuate that response? We tested whether each of these phases of the host response contributed to threespine sticklebacks' recently evolved resistance to their tapeworm <i>Schistocephalus solidus. </i>While marine stickleback and some susceptible lake fish permit fast-growing tapeworms, other lake populations are resistant and suppress tapeworm growth via a fibrosis response. We subjected lab-raised fish from three populations (susceptible marine 'ancestors', a susceptible lake population, a resistant lake population), to a novel immune challenge using an injection of: 1) a saline control, 2) alum, a generalized pro-inflammatory adjuvant that causes fibrosis, 3) a tapeworm protein extract, or 4) a combination of alum and tapeworm protein). With enough time, all three populations generated a robust fibrosis response to the alum treatments. Yet, only the resistant population exhibited a fibrosis response to the tapeworm protein alone. Thus, these populations differed in their ability to respond to the tapeworm protein but shared an intact fibrosis pathway. The resistant population also initiated fibrosis faster in response to alum, and was able to attenuate fibrosis, unlike the susceptible populations' slow but longer-lasting response to alum. As fibrosis has pathological side-effects that reduce fecundity, the faster recovery by the resistant population may reflect an adaptation to mitigate the costs of immunity. Broadly, our results confirm that parasite detection and immune initiation, activation speed, and immune attenuation simultaneously contribute to the evolution of parasite resistance and adaptations to infection in natural populations.</p>
Self-adjuvanting Nanovaccines Boost Lung-resident CD4+ T Cell Immune Responses in BCG-primed mice
<p>The "readcount_genename.xls" file and "fpkm_genename.xls" file contain gene expression data for genes (gene list is detailed in "gene.xls") in the panel. All data were obtained from bone marrow derived dendritic cells from WT C57BL/6 mice treated with KFE8 nanofibers or mock. All RNA sequencing and subsequent processing was performed by Novogene Corporation.</p> <p>The remaining .xls files contain the differential expression analysis for KFE8 nanofiber treatment at four hours compared with mock (NF4vsC4) or KFE8 nanofiber treatment at sixteen hours compared with mock (NF16vsC16).</p> <p>The "pathway analysis Rcode.R" file contains the code used to generate Reactome pathway analysis for both time points. </p> <p>The "NF16 volc Rcode.R" file contains the code used to generate a volcano plot for the 16 hour time point. </p>
Adaptive immune response selects for increased body size - dataset
<p>The dataset for the manuscript " Adaptive immune response selects for increased body size ". The dataset is packed in ZIP archive 'Dataset_Ejsmond_etal_2022.zip' with variables and description of variables saved in Matlab workspaces.</p>
Raw Data for the article: Klebsiella pneumoniae Lipopolysaccharides Serotype O2afg Induce Poor Inflammatory Immune Responses Ex Vivo
<p>Currently, <em>Klebsiella pneumoniae</em> is a pathogen of clinical relevance due to its plastic ability of acquiring resistance genes to multiple antibiotics. During <em>K. pneumoniae</em> infections, lipopolysaccharides (LPS) play an ambiguous role as they both activate immune responses but can also play a role in immune evasion. The LPS O2a and LPS O2afg serotypes are prevalent in most multidrug resistant <em>K. pneumoniae</em> strains. Thus, we sought to understand if those two particular LPS serotypes were involved in a mechanism of immune evasion. We have extracted LPS (serotypes O1, O2a and O2afg) from <em>K. pneumoniae</em> strains and, using human monocytes ex vivo, we assessed the ability of those LPS antigens to induce the production of pro-inflammatory cytokines and chemokines. We observed that, when human monocytes are incubated with LPS serotypes O1, O2a or O2afg strains, O2afg and, to a lesser extent, O2a but not O1 failed to elicit the production of pro-inflammatory cytokines and chemokines, which suggests a role in immune evasion. Our preliminary data also shows that nuclear translocation of NF-κB, a process which regulates an immune response against infections, occurs in monocytes incubated with LPS O1 and, to a smaller extent, with LPS O2a, but not with the LPS serotype O2afg. Our results indicate that multidrug resistant <em>K. pneumoniae</em> expressing LPS O2afg serotypes avoid an initial inflammatory immune response and, consequently, are able to systematically spread inside the host unharmed, which results in the several pathologies associated with this bacterium.</p>
Raw Data for the article: Impaired anti-SARS-CoV-2 humoral and cellular immune response induced by Pfizer-BioNTech BNT162b2 mRNA vaccine in solid organ transplanted patients
<p>SARS‐CoV‐2 vaccine is considered the primary health strategy able to end the current COVID‐19 pandemic. This viral infection impacts more severely solid organ transplant recipients (SOTRs) than general population, but the effect of vaccination in this subgroup of immunosuppressed patients is not known due to their exclusion from vaccination trials. Preliminary reports suggest a lower antibody production after BNT162b2 Pfizer/BioNTech mRNA‐vaccine,<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222937/#ajt16702-bib-0001"> 1 </a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222937/#ajt16702-bib-0002">2 </a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222937/#ajt16702-bib-0003">3 </a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222937/#ajt16702-bib-0004">4 </a>but no data are currently available on the elicited virus‐specific T cell responses.</p>
Dataset for the manuscript: Modelling the within-host spread of SARS-CoV-2 infection, and the subsequent immune response, using a hybrid, multiscale, individual-based model. Part I: Macrophages.
<p>Dataset for the manuscript:</p> <p>Modelling the within-host spread of SARS-CoV-2 infection, and the subsequent immune response, using a hybrid, multiscale, individual-based model. Part I: Macrophages. preprint, bioRxiv, 2022. DOI: 10.1101/2022.05.06.490883</p> <p>Each zip file contains the raw computational data (as a gzip compressed tarball), YAML input files, as well as Python plotting scripts. The Python plotting scripts have dependencies on the packages: <em>tarfile</em>, <em>multiprocessing</em>, <em>numpy</em>, <em>scipy</em>, and <em>matplotlib</em>. Note that the Python plotting scripts plot directly from the gzip compressed tarballs.</p> <p>The corresponding code can be found on GitHub: https://github.com/Ruth-Bowness-Group/CAModel</p>
Response to immune checkpoint blockade improved in pre-clinical model of breast cancer after bariatric surgery
<p>Bariatric surgery is becoming more prevalent as a sustainable weight loss approach, with vertical sleeve gastrectomy (VSG) being the first line of surgical intervention. We and others have shown that obesity exacerbates tumor growth while diet-induced weight loss impairs obesity-driven progression. It remains unknown how bariatric surgery-induced weight loss impacts cancer progression or alters responses to therapy. Using a pre-clinical model of diet induced obesity followed by VSG or diet-induced weight loss, breast cancer progression and immune checkpoint blockade therapy was investigated. Weight loss by bariatric surgery or weight matched dietary intervention before tumor engraftment protected against obesity-exacerbated tumor progression. However, VSG was not as effective as dietary intervention in reducing tumor burden despite achieving similar extent of weight and adiposity loss. Circulating leptin did not associate with changes in tumor burden. Uniquely, tumors in mice that received VSG displayed elevated inflammation and checkpoint ligand PD-L1. Further, mice that received VSG had reduced tumor infiltrating T lymphocytes suggesting an ineffective anti-tumor microenvironment. VSG-associated elevation of PD-L1 prompted us to next investigate the efficacy of immune checkpoint inhibitors in lean, obese, and formerly obese mice that lost weight by VSG or weight matched controls. While obese mice were resistant to immunotherapy, anti-PD-L1 potently impaired tumor progression after VSG through improved anti-tumor immunity. Thus, in formerly obese mice, surgical weight loss followed by immunotherapy reduced breast cancer burden. Further studies are necessary to determine how bariatric surgery sensitizes tumors to immune checkpoint inhibition.</p>
Heritability and genome-wide association study of vaccine-induced immune response in Beagles: A pilot study
<p>Both genetic and non-genetic factors contribute to individual variation in the immune response to vaccination. Understanding how genetic background influences variation in both the magnitude and persistence of vaccine-induced immunity is vital for improving vaccine development and identifying possible causes of vaccine failure. Dogs provide a relevant biomedical model for investigating mammalian vaccine genetics; canine breed structure and long linkage disequilibrium simplify genetic studies in this species compared to humans. The objective of this study was to estimate the heritability of the antibody response to vaccination against viral and bacterial pathogens and to identify genes driving variation of the immune response to vaccination in Beagles. Sixty puppies were immunized following a standard vaccination schedule with an attenuated combination vaccine containing antigens for canine adenovirus type 2, canine distemper virus, canine parainfluenza virus, canine parvovirus, and four strains of <em>Leptospira</em> bacteria. Serum antibody measurements for each viral and bacterial component were measured at multiple time points. Heritability estimations and GWAS were conducted using SNP genotypes at 279,902 markers together with serum antibody titer phenotypes. The heritability estimates were: (1) to <em>Leptospira</em> antigens, ranging from 0.178 to 0.628; and (2) to viral antigens, ranging from 0.199 to 0.588. There was not a significant difference between the overall heritability of vaccine-induced immune response to <em>Leptospira</em> antigens compared to viral antigens. Genetic architecture indicates that SNPs of low to high effect contribute to immune response to vaccination. GWAS identified two genetic markers associated with vaccine-induced immune response phenotypes. Collectively, these findings indicate that genetic regulation of the immune response to vaccination is antigen-specific and influenced by multiple genes of small effect.</p>
Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines
<p>Online Supplementary Dataset of the manuscript "Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines"</p>
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.