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Single-cell RNA-seq (scRNA-seq) is a powerful genomics technology to interrogate the cellular composition and behaviors of complex systems. While the number of scRNA-seq datasets and available computational analysis tools have grown exponentially, there are limited systematic data sharing strategies to allow rapid exploration and re-analysis of single-cell datasets, particularly in the cardiovascular field. We previously introduced PlaqView, an open-source web portal for the exploration and analysis of published atherosclerosis single-cell datasets. Now, we introduce PlaqView 2.0 (www.plaqview.com), which provides expanded features and functionalities as well as additional cardiovascular single-cell datasets. We showcase improved PlaqView functionality, backend data processing, user-interface, and capacity. PlaqView brings new or improved tools to explore scRNA-seq data, including gene query, metadata browser, cell identity prediction, ad hoc RNA-trajectory analysis, and drug-gene interaction prediction. PlaqView serves as one of the largest central repositories for cardiovascular single-cell datasets, which now includes data from human aortic aneurysm, gene-specific mouse knockouts, and healthy references. PlaqView 2.0 brings advanced tools and high-performance computing directly to users without the need for any programming knowledge. Lastly, we outline steps to generalize and repurpose PlaqView's framework for single-cell datasets from other fields.

Over the last few years, new high-throughput biotechnologies and bioinformatic methods are revolutionizing our way of deep profiling tissue specimens at the molecular levels. These recent innovations provide opportunities to advance our understanding of atherosclerosis using human lesions aborted during autopsies and cardiac surgeries. Studies on human lesions have been focusing on understanding the relationship between molecules in the lesions with tissue morphology, genetic risk of atherosclerosis, and future adverse cardiovascular events. This review will highlight ways to utilize human atherosclerotic lesions in translational research by work from large cardiovascular biobanks to tissue registries. We will also discuss the opportunities and challenges of working with human atherosclerotic lesions in the era of next-generation sequencing.