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12,799 results for “Immunization”
Data generated for the manuscript: "Increased 'selfness' in the tumor emerges as a possible immune scuplting mechanism: A pan-cancer data analysis of 32 solid tumors in TCGA"
<p>This submission has processed data generated for the manuscript: "Increased 'selfness' in the tumor emerges as a possible immune scuplting mechanism: A pan-cancer data analysis of 32 solid tumors in TCGA".</p> <p>The `data` folder contains processed information for the Human Protein Atlas (HPA) and The Cancer Genome Atlas (TCGA) datasets. The HPA data is found in `data/hpa` and contains gene ranks used to compute the thymus-likeness score (TLS) and files where the TLS has been calculated for the HPA tissues. The TCGA data can be found in `data/proc`, where individual RDS files have been given for each analyzed cohort. These RDS files contain the results of the cutoff scanning procedure mentioned in the manuscript and account for the bulk of the data generated for this study. RDS files can be loaded using the `readRDS` function in an R session. Other information used to create plots is in the `data` folder.</p> <p>The `plots` folder contain the result of plotting the entireity of the cutoff scanning procedure. The manuscript only contains plots for the 28 cohorts where a significant difference in terms of immune difference is observed, and that too, only the final heuristic plots. The `plots/tcga/immuneres` folder has plots at different levels: (i) single cell category/single deconvolution method with permutation tests (ii) single cell category/multiple deconvolution methods and (iii) significant cell categories/representative deconvolution method. Only (iii) is present in the manuscript. Overall, this folder should contain ~2000 plots.</p> <p>The code used to generate this study is deposited at: https://gitlab.com/narencs179/thymus-like-score</p>
RNA sequencing code associated with Billipp et al. Immunity 2024 - Chat + vs Chat - tuft cells
<p>R code and result for RNA-sequencing analysis comparing <em>Chat(GFP)+ </em>and <em>Chat(GFP)- </em>tuft cells sorted from the small intestine of <em>B6.Chat-GFP</em> mice. Associated with Billipp et al. Immunity 2024 titled "Tuft cell-derived acetylcholine promotes epithelial chloride secretion and intestinal helminth clearance"</p>
RNA sequencing code associated with Billipp et al. Immunity 2024 - Prox vs. distal tuft cells
<p>R code and result for RNA-sequencing analysis comparing tuft cells sorted from the proximal and distal small intestine of mice. Associated with Billipp et al. Immunity 2024 titled "<span>Tuft cell-derived acetylcholine promotes epithelial chloride secretion and intestinal helminth clearance</span>"</p>
Data from: Immune Transcriptional Response in Head Kidney Primary Cell Cultures Isolated from the Three Most Important Species in Chilean Salmonids Aquaculture.
<p>Data from Immune Transcriptional Response in Head Kidney Primary Cell Cultures Isolated from the Three Most Important Species in Chilean Salmonids Aquaculture. Files in .JBN and .xlsx format</p>
Immune Gene Repertoire of Soft Scale Insects (Hemiptera: Coccidae)
<p>Dataset (fasta sequences and alignments) referred to the manuscript "<span>Immune Gene Repertoire of Soft Scale Insects (Hemiptera: Coccidae)"</span></p> <p><strong><span>Abstract: </span></strong><span>Insects possess an effective immune system which has been extensively characterized in several model species, revealing a plethora of conserved genes involved in recognition, signaling and response to pathogens and parasites. However, some taxonomic groups, characterized by peculiar trophic niches, such as plant-sap feeders, which are often important pests of crops and forestry ecosystems, have been largely overlooked regarding their immune gene repertoire. Here we annotated the immune genes of soft scale insects (Hemiptera: Coccidae), for which omics data are publicly available. By using immune genes of aphids and <em>Drosophila</em> to query the genome of <em>Ericerus pela</em>, as well as the transcriptomes of <em>Ceroplastes cirripediformis</em> and <em>Coccus</em> sp., we pointed out the lack of peptidoglycan recognition proteins, galectins, thaumatins and antimicrobial peptides in Coccidae</span><span>. This work contributes to expand our knowledge about the evolutionary trajectories of immune genes and offers a list of promising candidates for developing new control strategies based on the suppression of pests’ immunity through RNAi technologies.</span></p>
Biomarkers in Metastatic Castration-Resistant Prostate Cancer for efficiency of Immune Checkpoint Inhibitors
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Transcriptome analysis of immune-inflammatory regulation in Tremella Fuciformis-derived Polysaccharide reeducated B16 cells subcutaneous model
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Colorectal cancer patients-derived immunity-organoid platform unveils cancer-specific tissue markers associated with immunotherapy resistance.
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Blood memory CD8 T cell phenotypes in lung cancer patients predict immune checkpoint treatment responses
<p>Rscript for figure generation and data analysis:</p> <p>GenerateFigures.R</p> <p> </p> <p>Seurat objects containing processed data after quality control:</p> <p><a href="../api/records/10867209/draft/files/NCCS_For_Zenodo.RDS/content" target="_blank" rel="noopener noreferrer">NCCS_For_Zenodo.RDS</a> - NCCS discovery cohort.</p> <p><a href="../api/records/10867209/draft/files/Pavia_For_Zenodo.RDS/content" target="_blank" rel="noopener noreferrer">Pavia_For_Zenodo.RDS</a> - Pavia validation cohort.</p> <p> </p> <p>RDS files containing DEGs or differentially abundant surface markers:</p> <p>TestResults2Groups.rds - Cell type specific LTR vs Non Responder DEG </p> <p>TestResults2GroupsADT.rds - Cell type specific LTR vs Non Responder differential surface markers</p> <p>TestResults2GroupsLungOnly.rds - Cell type specific LTR vs Non Responder DEG on lung samples only</p> <p>TestResults2GroupsLungOnlyADT.rds - Cell type specific LTR vs Non Responder differential surface markers on lung samples only</p> <p>TestResults3Groups.rds - Cell type specific LTR vs R vs Non Responder differential DEG</p> <p>TestResults3GroupsGeneralADT.rds - Across cell type LTR vs R vs Non Responder differential surface markers</p> <p>TestResults2GroupsGeneralRNA.rds - Across cell type LTR vs Non Responder DEG </p> <p>TestResults2GroupsGeneralADT.rds - Across cell type LTR vs Non Responder differential surface markers</p> <p>TestResults2GroupsLungOnlyGeneralRNA.rds - Across cell type LTR vs Non Responder DEG on lung samples only</p> <p>TestResults2GroupsLungOnlyGeneralADT.rds - Across cell type LTR vs Non Responder differential surface markers on lung samples only</p> <p>TestResults3GroupsGeneralRNA.rds - Across cell type LTR vs R vs Non Responder differential DEG</p> <p>TestResults3GroupsGeneralADT.rds - Across cell type LTR vs R vs Non Responder differential surface markers</p> <p> </p> <p>Logistic regression models trained on the NCCS discovery cohort:</p> <p>PerCellPredictions <CellType> * - Celltype specific models predicting either LTR, R or control group trained on all NCCS samples</p> <p>PerCellPredictions_2Groups_LungOnly <CellType> * - Celltype specific models predicting either LTR or NonResponder group, trained on lung samples only.</p> <p>PerCellPredictions_2Groups_<CellType> * - Celltype specific models predicting either LTR or NonResponder trained on all NCCS samples</p>
The immune landscape of murine skeletal muscle regeneration and aging
<p>This repository contains data associated with the publication Sousa, N.S. <em>et al.</em> (2024) ‘The immune landscape of murine skeletal muscle regeneration and aging’, <em>Cell Reports</em>, 43(11), p. 114975. doi:10.1016/j.celrep.2024.114975.</p> <p>The files are the following: </p> <ul> <li><a href="https://zenodo.org/api/records/14197888/draft/files/srt-all-samples.rds/content" target="_blank" rel="noopener noreferrer">srt-all-samples.rds</a> contains an RDS Seurat object with the dataset comprising all samples and all cells. Metadata, dimensionality reduction coordinates and clustering analysis results reported in the publication are also included.</li> <li><a href="https://zenodo.org/api/records/14197888/draft/files/srt-macs.rds/content" target="_blank" rel="noopener noreferrer">srt-macs.rds</a> contains an RDS Seurat object with the dataset comprising the subset of monocytes and macrophages across all samples. Metadata, dimensionality reduction coordinates and clustering analysis results reported in the publication are also included</li> <li><a href="https://zenodo.org/api/records/14197888/draft/files/metadata_all_samples.txt/content" target="_blank" rel="noopener noreferrer">metadata_all_samples.txt</a> is a table with metadata associated with the dataset comprising all samples. </li> <li><a href="https://zenodo.org/api/records/14197888/draft/files/metadata_macs.txt/content" target="_blank" rel="noopener noreferrer">metadata_macs.txt</a> is a table with metadata associated with the dataset comprising the subset of monocytes and macrophages across all samples. </li> </ul> <p> </p> <div> </div> <p> </p>
Unveiling genetic signatures of immune response in immune-related diseases through single-cell eQTL analysis across diverse conditions
<p><em><strong>Unveiling genetic signatures of immune response in immune-related diseases through single-cell eQTL analysis across diverse conditions</strong></em></p> <p> </p> <p>Tools and scripts were used to generate results in Zhang et al 2024.</p> <p>Supplementary files that were not included in the initial submission.</p> <p>Full summary statistics of eQTLs including top eQTLs and all SNP-gene pairs of each cell type, consistent.tar.gz for consistent eQTLs per cell and response.tar.gz for response eQTLs, respectively.</p>
Upfront whole blood transcriptional patterns in patients receiving immune checkpoint inhibitors associate with clinical outcome
<p>This repository contains supplementary materials for the research paper "Upfront whole blood transcriptional patterns in patients receiving immune checkpoint inhibitors associate with clinical outcome". The materials are organized in the following folders:</p> <ul> <li>01_code: code to reproduce the results</li> <li>02_raw_data_public: raw gene count data of the 14,085 whole blood transcriptomes from public datasets (PUBLIC)</li> <li>03_raw_data_primero: raw gene count data of the 145 pre-ICI whole blood samples from the PRIMERO cohort, including sample annotation with response data ("primero_sample_anno.tsv")</li> <li>04_ica: results of the independent component analysis on the PUBLIC dataset, including the transcriptional components ("ica_public_flipped_consensus_independent_components.tsv"), the gene set enrichment analysis results on these components, and the projected activities of the PRIMERO samples for these transcriptional components ("ica_primero_mixing_matrix_projected_corrected.tsv")<br><br></li> </ul>
Isolating human monoclonal antibodies against adeno-associated virus from donors with pre-existing immunity
<p>With the advent of single B-cell cloning technology, we can isolate antibodies against virtually any antigen to study the interaction of a given pathogen with the immune system and develop novel therapeutic strategies. Antibodies directed against the capsid of adeno-associated viruses (AAV) are a significant obstacle to effectively leveraging AAV as a gene-delivery vector in seropositive individuals. In order to design next-generation vectors that can evade neutralization by these antibodies, studies have mapped the epitopes of mousemonoclonal antibodies generated by immunization with AAV. Although these studies provide critical information regarding capsid immunogenicity, they cannot address (1) differences in the antibody repertoire generated in humans following AAV natural infection; or (2) how reactions can vary when generated in response to vector administration. Here, we isolated and evaluated a panel of novel, fully human anti-AAV antibodies by cloning single memory B cells from a seropositive normal donor. We have validated the utility of this approach to study AAV immunology. Our goal is to leverage this knowledge to design novel AAV variants that can effectively transduce target tissues in individuals with AAV-neutralizing antibodies.</p>
Mating stimulates the immune response and sperm storage-related genes expression in spermathecae of bumblebee (Bombus terrestris) queen
<p>Data of the genes expression in spermathecae of mated bumblebee (<em>Bombus terrestris</em>) queen</p>
Subtle alterations in neonatal neurodevelopment following early or late exposure to prenatal maternal immune activation
<p>Structural MRI</p>
Long-term memory T cells as preventive anticancer immunity elicited by TuA-derived heteroclitic peptides
<p>The host’s immune system may be primed against antigens during the lifetime (e.g. microorganisms antigens—MoAs), and swiftly<br> recalled upon growth of a tumor expressing antigens similar in sequence and structure. C57BL/6 mice were immunized in a preventive<br> setting with tumor antigens (TuAs) or corresponding heteroclitic peptides specific for TC-1 and B16 cell lines. AQ1 Immediately or 2-<br> months after the end of the vaccination protocol, animals were implanted with cell lines. The specific anti-vaccine immune response as<br> well as tumor growth were regularly evaluated for 2 months post-implantation. The preventive vaccination with TuA or their<br> heteroclitic peptides (hPep) was able to delay (B16) or completely suppress (TC-1) tumor growth when cancer cells were implanted<br> immediately after the end of the vaccination. More importantly, TC-1 tumor growth was significantly delayed, and suppressed in 6/8<br> animals, also when cells were implanted 2-months after the end of the vaccination. The vaccine-specific T cell response provided a<br> strong immune correlate to the pattern of tumor growth. A preventive immunization with heteroclitic peptides resembling a TuA is able<br> to strongly delay or even suppress tumor growth in a mouse model. More importantly, the same effect is observed also when tumor<br> cells are implanted 2 months after the end of vaccination, which corresponds to 8 – 10 years in human life. The observed potent tumor<br> control indicates that a memory T cell immunity elicited during the lifetime by a antigens similar to a TuA, i.e. viral antigens, may<br> ultimately represent a great advantage for cancer patients and may lead to a novel preventive anti-cancer vaccine strategy.</p>
Serial seroprevalence study: follow-up of immunity to SARS-Cov-2 infection and monitoring of effective vaccination coverage, in three Chilean cities
<p>Population-based serosurvey in Santiago, Talca, and Coquimbo–La Serena </p>
Supplementary Materials for Evaluation role of ferroptosis long non-coding RNAs for immune microenvironment and microsatellite instability in colon cancer
<p>Supplementary Materials for "Evaluation role of ferroptosis long non-coding RNAs for immune microenvironment and microsatellite instability in colon cancer"</p>
Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants
<p>Scripts and metadata used in the analysis of the manuscript, <em>Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants.</em></p>
Differences in local immune cell landscape between Q fever and atherosclerotic abdominal aortic aneurysms identified by multiplex immunohistochemistry
<p><strong>Background:</strong> Chronic Q fever is a zoonosis caused by the bacterium <em>Coxiella burnetii</em> which can manifest as infection of an abdominal aortic aneurysm (AAA). Antibiotic therapy often fails, resulting in severe morbidity and high mortality. Whereas previous studies have focused on inflammatory processes in blood, the aim of this study was to investigate local inflammation in aortic tissue.</p> <p><strong>Methods:</strong> Multiplex immunohistochemistry was used to investigate local inflammation in Q fever AAAs compared to atherosclerotic AAAs in aorta tissue specimen. Two six-plex panels were used to study both the innate and adaptive immune system.</p> <p><strong>Results: </strong>Q fever AAAs and atherosclerotic AAAs contained similar numbers of CD68<sup>+</sup> macrophages and CD3<sup>+</sup> T cells. However, in Q fever AAAs the number of CD68<sup>+</sup>CD206<sup>+</sup> M2 macrophages was increased, while expression of GM-CSF was decreased compared to atherosclerotic AAAs. Furthermore, Q fever AAAs showed an increase in both the number of CD8<sup>+</sup> cytotoxic T cells and CD3<sup>+</sup>CD8<sup>-</sup>FoxP3<sup>+</sup> regulatory T cells. Lastly, Q fever AAAs did not contain any well-defined granulomas.</p> <p><strong>Conclusions:</strong> These findings demonstrate that despite the presence of pro-inflammatory effector cells, persistent local infection with <em>C. burnetii</em> is associated with an immune suppressed micro environment.</p> <p><strong>Funding:</strong> This work was supported by SCAN consortium: European Research Area - CardioVascualar Diseases (ERA-CVD) grant [JTC2017-044] and TTW-NWO open technology grant [STW-14716].</p>
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Allen Brain Atlas
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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.