PUBLICATION
A 3D Atlas of Hematopoietic Stem and Progenitor Cell Expansion by Multi-dimensional RNA-Seq Analysis
- Authors
- Xue, Y., Liu, D., Cui, G., Ding, Y., Ai, D., Gao, S., Zhang, Y., Suo, S., Wang, X., Lv, P., Zhou, C., Li, Y., Chen, X., Peng, G., Jing, N., Han, J.J., Liu, F.
- ID
- ZDB-PUB-190507-6
- Date
- 2019
- Source
- Cell Reports 27: 1567-1578.e5 (Journal)
- Registered Authors
- Liu, Feng, Lv, Peng, Zhang, Yifan
- Keywords
- 3D atlas, hematopoietic stem and progenitor cell, multi-dimensional RNA-seq, signaling, zebrafish
- Datasets
- GEO:GSE120581, GEO:GSE120503, GEO:GSE120509, GEO:GSE120578
- MeSH Terms
-
- Animals
- Hematopoiesis*
- Hematopoietic Stem Cells/classification
- Hematopoietic Stem Cells/cytology*
- Hematopoietic Stem Cells/metabolism
- RNA-Seq
- Signal Transduction
- Single-Cell Analysis
- Stem Cell Niche
- Transcriptome*
- Zebrafish
- PubMed
- 31042481 Full text @ Cell Rep.
Citation
Xue, Y., Liu, D., Cui, G., Ding, Y., Ai, D., Gao, S., Zhang, Y., Suo, S., Wang, X., Lv, P., Zhou, C., Li, Y., Chen, X., Peng, G., Jing, N., Han, J.J., Liu, F. (2019) A 3D Atlas of Hematopoietic Stem and Progenitor Cell Expansion by Multi-dimensional RNA-Seq Analysis. Cell Reports. 27:1567-1578.e5.
Abstract
In vertebrates, hematopoiesis occurring in different niches is orchestrated by intrinsic and extrinsic regulators. Previous studies have revealed numerous linear and planar regulatory mechanisms. However, a multi-dimensional transcriptomic atlas of any given hematopoietic organ has not yet been established. Here, we use multiple RNA sequencing (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 to understand HSPC expansion in an intact vertebrate hematopoietic organ.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping