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Alveolar echinococcosis (AE) is caused by the chronic infection of E. multilocularis, whose tumor-like growth can lead to high fatality if improperly treated. The early diagnosis of infection and the treatment of advanced AE remain challenging. Herein, bulk RNA-seq, scRNA-seq, and spatial transcriptomics technologies are integrated, to reveal the host immune response mechanism against E. multilocularis both spatially and chronologically, collecting mouse liver samples at multiple timepoints up to 15 months post infection. These results unveil an unprecedented high-resolution spatial atlas of the E. multilocularis infection foci and the functional roles of neutrophils, Spp1+ macrophages, and fibroblasts during disease progression. The heterogeneity of neutrophil and macrophage subpopulations are critical in both parasite-killing and the occurrence of immunosuppression during AE progression. These findings indicate the transition of parasite control strategy from "active killing" to "negative segregation" by the host, providing instructive insights into the treatment strategy for echinococcosis.
Pubmed ID: 39985260
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Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.
View all literature mentionsThe Office of Public Health Genomics (OPHG) aims to integrate genomics into public health research, policy, and programs. Doing so could improve interventions designed to prevent and control the country''s leading chronic, infectious, environmental, and occupational diseases. OPHG''s efforts focus on conducting population-based genomic research, assessing the role of family health history in disease risk and prevention, supporting a systematic process for evaluating genetic tests, translating genomics into public health research and programs, and strengthening capacity for public health genomics in disease prevention programs. Goals: To improve public health interventions of diseases of major public health importance, including chronic, infectious, environmental, and occupational diseases, through six major initiatives: * Evaluation of Genomic Applications in Practice and Prevention (EGAPP), * Human Genome Epidemiology Network (HuGENet), * NHANES Collaborative Genomics Project, * Family History Public Health Initiative, * Genomics Translation Research and Programs, and, * Genomic Applications in Practice and Prevention Network (GAPPNet).
View all literature mentionsOpen source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.
View all literature mentionsMulti-threaded software for rapid quality control and preprocessing of high throughput sequencing data specified for different experiments. It consists of four modules that speed up the report on statistics graphs of raw datasets, preprocessed datasets and preprocessing status.
View all literature mentionsSoftware package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
View all literature mentionsSoftware as R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data.
View all literature mentionsWeb tool for graphical illustrations for biological systems by BioRender. Used for articles and presentations. Collection of pre made icons and templates from life science fields for scientific illustrations. Customized icons possible on request.
View all literature mentionsPortal to search liver single cell RNA-sequencing datasets. Datasets for expression of genes or proteins (when CITE-seq was performed). To search for gene enter the official gene name. To search for protein please click to see specific names to use for different markers included.
View all literature mentionslaboratory mouse with name BALB/cAnNCrl from MGI.
View all literature mentionsCentral data repository for nematode biology including complete genomic sequence, gene predictions and orthology assignments from range of related nematodes.Data concerning genetics, genomics and biology of C. elegans and related nematodes. Derived from initial ACeDB database of C. elegans genetic and sequence information, WormBase includes genomic, anatomical and functional information of C. elegans, other Caenorhabditis species and other nematodes. Maintains public FTP site where researchers can find many commonly requested files and datasets, WormBase software and prepackaged databases.
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