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Series GSE142392 Query DataSets for GSE142392
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
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.
 
Overall design Analysis of monocytes differentiating into macrophages
 
Contributor(s) Slavov N
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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
Submission date Dec 19, 2019
Last update date Dec 22, 2019
Contact name Nikolai Slavov
Organization name Northeastern University
Lab Slavov Lab
Street address 360 Huntington Avenue
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (2)
GSM4226877 mixed monocytes (U937 cell line) and macrophages rep1
GSM4226878 mixed monocytes (U937 cell line) and macrophages rep2
Relations
BioProject PRJNA596807
SRA SRP238267

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE142392_RAW.tar 54.4 Mb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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