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Gigascience. 2019 May 1;8(5). pii: giz047. doi: 10.1093/gigascience/giz047.

Single-cell transcriptomic landscape of nucleated cells in umbilical cord blood.

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School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China.
BGI-Shenzhen, Shenzhen 518083, China.
Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518035, Guangdong Province, China.
Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China.
James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.
Department of Immunology and Microbiology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China.



For both pediatric and adult patients, umbilical cord blood (UCB) transplant is a therapeutic option for a variety of hematologic diseases, such as blood cancers, myeloproliferative disorders, genetic diseases, and metabolic disorders. However, the level of cellular heterogeneity and diversity of nucleated cells in UCB has not yet been assessed in an unbiased and systemic fashion. In the present study, nucleated cells from UCB were subjected to single-cell RNA sequencing to simultaneously profile the gene expression signatures of thousands of cells, generating a rich resource for further functional studies. Here, we report the transcriptomes of 17,637 UCB cells, covering 12 major cell types, many of which can be further divided into distinct subpopulations.


Pseudotemporal ordering of nucleated red blood cells identifies wave-like activation and suppression of transcription regulators, leading to a polarized cellular state, which may reflect nucleated red blood cell maturation. Progenitor cells in UCB also comprise 2 subpopulations with activation of divergent transcription programs, leading to specific cell fate commitment. Detailed profiling of cytotoxic cell populations unveiled granzymes B and K signatures in natural killer and natural killer T-cell types in UCB.


Taken together, our data form a comprehensive single-cell transcriptomic landscape that reveals previously unrecognized cell types, pathways, and mechanisms of gene expression regulation. These data may contribute to the efficacy and outcome of UCB transplant, broadening the scope of research and clinical innovations.


natural killer T cell; nucleated red blood cell; single-cell RNA sequencing; transcriptomics; umbilical cord blood

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