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:GSE120503, GEO:GSE120581, GEO:GSE120578, GEO:GSE120509
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.
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
Figures
Show all Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes