Multi-Modal Cell Profiling and Data Integration to Atlas the Immune System

This project will develop a set of generalizable tools, resources, and best practices for multi-modal cell and tissue phenotyping, integrating high-throughput and spatially resolved methods applied to tissues of the human immune system.

This group developed technologies for multi-modal profiling of single cells and analysis tools to harmonize and analyze them. They generated large reference datasets of the human immune system, alongside new computational methods for analyzing multimodal data and pooled genetic screens, including extensions to the analysis tool Seurat for single-cell genomics analysis and signac for single-cell chromatin analysis. They released an extensive RNA-sequencing dataset and chromatin accessibility dataset, and published four preprints to further investigate multimodal data analysis’ potential to uncover new biological insights.

Papers:

• Scalable, multimodal profiling of chromatin accessibility, gene expression, and protein levels in single cells
• Integrated analysis of multimodal single-cell data
• Characterizing the molecular regulation of inhibitory immune checkpoints with multi-modal single-cell screens
• Multimodal single-cell chromatin analysis with Signac