MassIVE MSV000084660

Partial Public

SCoPE2 expanded data sets 20191204


Please note most files are the "updates" subfolder. Processed protein and transcript data available at: The fate and physiology of individual cells are controlled by protein interactions. Yet, our ability to quantitatively analyze proteins in single cells has remained limited. To overcome this barrier,we developed SCoPE2. It introduces automated and miniaturized sample preparation, substantially increasing quantitative accuracy while lowering cost and hands-on time. These advances enabled us to analyze the emergence of cellular heterogeneity as homogeneous monocytes differentiated into macrophage-like cells in the absence of polarizing cytokines. SCoPE2 quantified over 2,700proteins in 1,018 single monocytes and macrophages in ten days of instrument time, and the quantified proteins allowed us to discern single cells by cell type. Furthermore, the data uncovered acontinuous gradient of proteome states for the macrophage-like cells, suggesting that macrophage heterogeneity may emerge even in the absence of polarizing cytokines. Parallel measurements of transcripts by 10x Genomics scRNA-seq suggest that SCoPE2 samples 20-fold more copies per gene, thus supporting quantification with improved count statistics. Joint analysis of the data indicated that most genes had similar responses at the protein and RNA levels, though the responses of hundreds of genes differed. Our methodology lays the foundation for automated and quantitative single-cell analysis of proteins by mass spectrometry. [doi:10.25345/C50D5J] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: SCoPE2 SCoPE-MS single cell RNA macrophage monocyte


Principal Investigators: Nikolai Slavov, Northeastern University, USA
Submitting User: hspecht
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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.
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Proteins quantified by submitted quantification results.
Proteins differentially abundant in submitted quantification results.