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90 results for “cytokine genes”
Supporting data for: Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines
<p><strong>SUMMARY OF THE STUDY</strong></p> <p>We combined functional genomics and human genetics to investigate processes that affect type 1 diabetes (T1D) risk by mediating beta-cell survival in response to proinflammatory cytokines. We mapped 38,931 cytokine-responsive candidate <em>cis-</em>regulatory elements (cCREs) in beta-cells using ATAC-seq and snATAC-seq and linked them to target genes using co-accessibility and HiChIP. Using a genome-wide CRISPR screen in EndoC-βH1 cells we identified 867 genes affecting cytokine-induced survival, and genes promoting survival and up-regulated in cytokines were enriched at T1D risk loci. Using SNP-SELEX, we identified 2,229 variants in cytokine-responsive cCREs altering transcription factor (TF) binding, and variants altering binding of TFs regulating stress, inflammation and apoptosis were enriched for T1D risk. At the 16p13 locus, a fine-mapped T1D variant altering TF binding in a cytokine-induced cCRE interacted with <em>SOCS1</em>, which promoted survival in cytokine exposure. Our findings reveal processes and genes acting in beta-cells during inflammation that modulate T1D risk.</p> <p><strong>DESCRIPTION OF FILES:</strong></p> <ul> <li>Supplementary Data 1. List of islet cCREs annotated with cell type and cytokine response - also in GSE205853</li> <li>Supplementary Data 2. Coaccessible sites in untreated beta cells and promoter annotations - also in GSE205853</li> <li>Supplementary Data 3. Coaccessible sites in cytokine-treated beta cells and promoter annotations - also in GSE205853</li> <li>Supplementary Data 4. Coaccessible sites in cytokine treated and untreated beta cells and promoter annotations - also in GSE205853</li> <li>Supplementary Data 5. Chromatin interactions in EndoC-BH1 cells - also in GSE205853</li> <li>Supplementary Data 6. Variants selected for SNP-SELEX assay </li> <li>Supplementary Data 7. Variants with TF binding and allelic binding results from SNP-SELEX</li> <li>Supplementary Data 8. snATAC-seq barcodes and metadata - also in GSE205853</li> <li>Supplementary Data 9. CRISPR-KO screen results - also in GSE205853</li> <li>Supplementary Data 10. Bulk ATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 11. Bulk RNA-seq count matrix - also in GSE205853</li> <li>Supplementary Data 12. Alpha cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 13. Acinar cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 14. Beta cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 15. Stellate cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 16. Endothelial cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 17. Delta cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 18. Luciferase assay rs10483809</li> <li>Supplementary Data 19. SOCS1 knockdown qPCR results</li> <li>Supplementary Data 20. SOCS1 knockdown Apotracker (flow-cytometry)results</li> </ul> <p><strong>Raw data deposited at GEO, accessions GSE205853 and GSE118725.</strong></p> <p><em>Please refer to publication and GEO for details on methods.</em></p>
Relationships between immune gene expression and circulating cytokine levels in wild house mice
<p>1. Quantitative PCR (qPCR) has been commonly used to measure gene expression in a number of research contexts, but the measured RNA concentrations do not always represent the concentrations of active proteins which they encode. This can be due to transcriptional regulation or post-translational modifications, or localisation of immune environments, as can occur during infection. However, in studies using free-living non-model species, such as in ecoimmunological research, qPCR may be the only available option to measure a parameter of interest, and so understanding the quantitative link between gene expression and associated effector protein levels is vital.</p> <p>2. Here we use qPCR to measure concentrations of RNA from mesenteric lymph node (MLN) and spleen tissue, and multiplex ELISA of blood serum to measure circulating cytokine concentrations in a wild population of a model species, Mus musculus domesticus.</p> <p>3. Few significant correlations were found between gene expression levels and circulating cytokines of the same immune genes or proteins, or related functional groups. Where significant correlations were observed, these were most frequently within the measured tissue (i.e. the expression levels of genes measured from spleen tissue were more likely to correlate with each other rather than with genes measured from MLN tissue, or with cytokine concentrations measured from blood).</p> <p>4. Potential reasons for discrepancies between measures, including differences in decay rates and transcriptional regulation networks are discussed. We highlight the relative usefulness of different measures under different research questions, and consider what might be inferred from immune assays.</p>
Data from: Short-term sleep loss alters cytokine gene expression in brain and peripheral tissues and increases plasma corticosterone of zebra finch (Taeniopygia guttata)
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Relationships between immune gene expression and circulating cytokine levels in wild house mice
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Gene Expression Of Suppressor Of Cytokines in In Cutaneous Warts
ClinicalTrials.gov study NCT05781841. IPD Sharing: NO. Countries: 1. Publications: 1.
Investigating Cytokine Genes of Stem Cell Donors
ClinicalTrials.gov study NCT00353821. IPD Sharing: Not stated. Countries: 1. Publications: 3.
NFAT-Dependent Cytokine Gene Expression for Immune Monitoring in Kidney Transplant Patients
ClinicalTrials.gov study NCT01771705. IPD Sharing: Not stated. Countries: 1. Publications: 7.
Depression, Genes, Cytokines, Chronic Fatigue, Physical Illnesses and Quality of Life
ClinicalTrials.gov study NCT02943330. IPD Sharing: NO. Countries: 0. Publications: 39.
Impact of Maternal Immune Activation and Sex on Placental and Fetal Brain Cytokine and Gene Expression Profiles in a Preclinical Model of Neurodevelopmental Disorders
GEO Series GSE248222. Mus musculus. 64 samples. Type: Expression profiling by high throughput sequencing.
The cytokine DIEDEL and a viral homologue suppress deleterious IMD-dependent gene expression in drosophila
GEO Series GSE68174. Drosophila melanogaster. 8 samples. Type: Expression profiling by array.
Exploration of specific gene expression behind the intercellular heterogeneity of type 2 cytokine secretion activity of Group 2 innate lymphoid cell (ILC2) isolated from peripheral blood of severe ast
GEO Series GSE213810. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes [RNA-seq]
GEO Series GSE110386. Homo sapiens. 45 samples. Type: Expression profiling by high throughput sequencing.
Zinc supplementation with or without additional micronutrients does not affect peripheral blood gene expression or serum cytokine level in Bangladeshi children
GEO Series GSE184998. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic analysis of porcine peripheral blood reveals differentially expressed genes from the cytokine-cytokine receptor interaction pathway related to health status
GEO Series GSE96640. Sus scrofa. 64 samples. Type: Expression profiling by high throughput sequencing.
Cytokine-sensing primary enhancer cluster launches secondary enhancers to activate multi-gene locus [RNA-seq]
GEO Series GSE127140. Mus musculus. 19 samples. Type: Expression profiling by high throughput sequencing.
Human Eosinophils Express a Distinct Gene Expression Program in Response to IL-3 Compared to Common Beta-Chain Cytokines IL-5 and GM-CSF
GEO Series GSE128027. Homo sapiens. 28 samples. Type: Expression profiling by high throughput sequencing.
Immune-Related Gene Expression and Cytokine Secretion is Reduced Among African American Colon Cancer Patients
GEO Series GSE146009. Homo sapiens. 65 samples. Type: Expression profiling by high throughput sequencing.
Expression data measured by custom Nanostring gene set of CD4+ T cells from healthy individuals stimulated with anti-CD3/CD28 with or without IFNb or Th17 polarizing cytokines
GEO Series GSE60341. Homo sapiens. 1950 samples. Type: Other.
Gene expression profiles of chimeric cytokine receptor-engineered CAR-T cells
GEO Series GSE216734. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes
GEO Series GSE110387. Homo sapiens. 63 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
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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.