Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology; Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration; Chinese Academy of Sciences (CAS)
Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology; Chinese Academy of Sciences (CAS), Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences (CAS)
Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology; Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration; Chinese Academy of Sciences (CAS)
Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology; Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology
Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology; Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration; Chinese Academy of Sciences (CAS)
Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology; Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences (CAS)
Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology; Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration; Chinese Academy of Sciences (CAS)
Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology; Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration; Chinese Academy of Sciences (CAS)
Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology; Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology
Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology; Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology
Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology; Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology
Chinese Academy of Sciences (CAS), Shanghai Institutes for Biological Sciences, Institute of Biochemistry and Cell Biology, State Key Laboratory of Cell Biology
Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology; Chinese Academy of Sciences (CAS), Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology ; Chinese Academy of Sciences (CAS)
Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology; Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration; Chinese Academy of Sciences (CAS)
In vertebrates, hematopoiesis occurring in different niches is orchestrated by intrinsic and extrinsic regulators, which are indispensable for the maintenance of homeostasis in a whole organism. Previous studies have revealed a large number of linear and planar regulatory mechanisms. However, a multi-dimensional transcriptomic atlas of any given hematopoietic organ has not been yet established. Here, we use multiple RNA-seq approaches, including cell type-specific temporal bulk RNA-seq, in vivo GEO-seq, and single-cell RNA-seq (scRNA-seq), to characterize the detailed spatiotemporal transcriptome during hematopoietic stem and progenitor cell (HSPC) expansion in the caudal hematopoietic tissue (CHT) of zebrafish. Combinatorial expression profiling reveals that in the CHT niche, HSPCs and their neighboring supporting cells are co-regulated by shared signaling pathways and intrinsic factors, such as integrin signaling and Smchd1. Moreover, scRNA-seq analysis unveils the strong association between cell cycle status and HSPC differentiation. Taken together, we report a global transcriptome landscape that provides valuable insights and a rich resource for understanding HSPC development, particularly on HSPC expansion in an intact hematopoietic organ. The key signaling pathways and factors identified here would contribute to HSPC expansion in vitro.
Keywords: Hematopoietic stem and progenitor cell, Multi-dimensional RNA-seq, 3D atlas, Signaling, Zebrafish
Xue, Yuanyuan and Liu, Denghui and Cui, Guizhong and Ding, Yanyan and Ai, Daosheng and Gao, Suwei and Zhang, Yifan and Suo, Shengbao and Wang, Xiaohan and Lv, Peng and Zhou, Chunyu and Li, Yizhou and Chen, Xingwei and Peng, Guangdun and Jing, Naihe and Han, Jing-Dong J. and Liu, Feng, A 3D Atlas of Hematopoietic Stem and Progenitor Cell Expansion by Multi-Dimensional RNA-Seq Analysis (February 8, 2019). Available at SSRN: https://ssrn.com/abstract=3331363 or http://dx.doi.org/10.2139/ssrn.3331363
This version of the paper has not been formally peer reviewed.
Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology
Shanghai China
Chinese Academy of Sciences (CAS), Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology
Shanghai China
Chinese Academy of Sciences (CAS)
Building 7, NO. 80 Zhongguancun Road Beijing, Beijing 100190 China
Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology
Shanghai China
Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology
Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology
Shanghai China
Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology
Shanghai China
Chinese Academy of Sciences (CAS)
Building 7, NO. 80 Zhongguancun Road Beijing, Beijing 100190 China
Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology
Shanghai China
Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology
Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology
Shanghai China
Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology
Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology
Shanghai China
Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology
Chinese Academy of Sciences (CAS), Shanghai Institutes for Biological Sciences, Institute of Biochemistry and Cell Biology, State Key Laboratory of Cell Biology
Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology ( email )
Shanghai China
Chinese Academy of Sciences (CAS), Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology ( email )
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