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| Status |
Public on Dec 20, 2019 |
| Title |
10x Genomics scRNA-seq from monocytes and macrophages |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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 lowers cost and hands-on time by introducing automated and miniaturized sample preparation while substantially increasing quantitative accuracy. 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 2,700 proteins 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 a continuous 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.
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| Overall design |
Analysis of monocytes differentiating into macrophages
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| Contributor(s) |
Slavov N |
| Citation |
Specht H, Emmott E, Petelski A, Huffman RG, Perlman D, Serra M, Kharchenko P, Koller A, Slavov N. (2019) Single-cell mass-spectrometry quantifies the emergence of macrophage heterogeneity bioRxiv DOI: 10.1101/665307
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| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| DP2 GM123497 |
Ribosome-mediated translational regulation during stem cell differentiation |
NORTHEASTERN UNIVERSITY |
Nikolai Slavov |
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| Submission date |
Dec 19, 2019 |
| Last update date |
Feb 28, 2021 |
| Contact name |
Nikolai Slavov |
| Organization name |
Northeastern University
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| Lab |
Slavov Lab
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| Street address |
360 Huntington Avenue
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (2) |
| GSM4226877 |
mixed monocytes (U937 cell line) and macrophages rep1 |
| GSM4226878 |
mixed monocytes (U937 cell line) and macrophages rep2 |
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| Relations |
| BioProject |
PRJNA596807 |
| SRA |
SRP238267 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE142392_RAW.tar |
54.4 Mb |
(http)(custom) |
TAR (of CSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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