Open resources and data from the Allen Institute: exploring immune health, rheumatoid arthritis, tissue immunity, and cytokine perturbations 2309948

Abstract

Abstract Introduction A core goal of the Allen Institute is to openly share our immunological data and enable the immunology community to explore and re-use data from our studies of human disease cohorts. We have profiled healthy adults and children as well as patients at risk for rheumatoid arthritis, with multiple myeloma, under treatment for melanoma, and with COVID-19 longitudinally for up to two years, then performed immune profiling using scRNA-seq, plasma or serum proteomics, and clinical lab tests. Methods To process, analyze, and distribute this data, we developed the Human Immune System Explorer (HISE) platform, a flexible, scalable, cloud-based framework to enable storage, interactive analysis, visualization, and generation of Certificates of Reproducibility that enable inspection and replay of any step of an analysis workflow. This platform enables us to openly provide data, interactive visualization tools, scientific context, and analysis methods with the broader immunology community. Results We have applied our tools to both our own studies and large publicly available data resources, including a dataset of ∼10 million PBMCs from a study with 90 cytokine perturbations. These tools and data are freely available to the public, including interactive differential expression, UMAP, clinical data, and longitudinal trend visualizations. Conclusion We invite immunologists to explore this resource and our expanding library of immunology data, insights, and tools at https://explore.allenimmunology.org/. Funding Source n/a Topic Categories Computational and Systems Immunology (COMP)