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Abstract
Background Single cell RNA sequencing (scRNA-seq) is a powerful technique for studying the molecular heterogeneity of cells.1–3 However, scRNA-seq does not provide information about protein expression, which is essential for understanding the functional state of cells.
Methods InTraSeq is a novel technology that allows for the simultaneous measurement of RNA and protein expression in single cells. InTraSeq uses validated and functionally tested antibodies to quantify extracellular, cytoplasmic, and nuclear proteins, as well as their post-translational modifications. The InTraSeq protocol is streamlined and requires only one hour of benchwork. It also allows for multi-day sample storage, making it a practical and efficient tool for high-throughput applications.
Results InTraSeq has been used to characterize a variety of cell types, including immune cells, stem cells, and cancer cells. In these studies, InTraSeq has been shown to provide a more comprehensive view of the cellular mechanisms of complex biology than scRNA-seq alone. For example, InTraSeq has been used to identify new cell subtypes, to map signaling pathways, and to track cell differentiation trajectories (figures 1–4).
Conclusions InTraSeq is a powerful new tool for studying the molecular heterogeneity of cells. It provides a more comprehensive view of the cellular mechanisms of complex biology than scRNA-seq alone. InTraSeq is a practical and efficient tool for high-throughput applications, and it has the potential to revolutionize our understanding of cell biology.
Acknowledgements We would like to thank the following CST employees for their contributions below.
Shivani Sheth, Tyler Levy, and Sean Beausoleil for their contributions in InTraSeq’s research and development.
Sasha Tkachev for his contributions in bioinformatics analyses.
Jeremy Fischer and Keith Arlotta for conjugation of InTraSeq antibodies.
References
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Blair JD, Hartman A, Zenk F, Dalgarno C, Treutlein B, Satija R. Phospho-seq: Integrated, multi-modal profiling of intracellular protein dynamics in single cells. bioRxiv. 2023:2023–03.
Lin Y, Wu TY, Wan S, Yang JY, Wong WH, Wang YR. scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning. Nature biotechnology. 2022 May;40(5):703–10.
InTraSeq preserves cellular heterogeneity
lnTraSeq quantifies and shows a robust signal of RNA and proteins in individual cells
lnTraSeq quantifies and shows a robust signal of RNA and proteins in individual cells
InTraSeq reveals unbiased PTMs expression correlation with RNA+protein in single cell technologies
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