The transcriptional landscape of mouse blood stem/progenitor cell transitions at single cell resolution

Current gene-expression databases for the haematopoietic system provide information on gene expression profiles present in bulk populations. Although informative, these studies lack the resolution that can be gained at a single-cell level. In particular, population-average data assumes homogeneity within the population and may as such obscure the ability to detect the heterogeneity of decision-making processes in individual cells. Here we report 1656 single cell transcriptomes analysed by single-cell RNA sequencing. Cells were FACS sorted on broad gates encompassing haematopoietic stem and progenitor populations (HSPCs), with index sorting data collected to permit retrospective identification of populations by surface marker expression. Our dataset thus represents the gene expression landscape of HSPCs at single-cell resolution, capturing the heterogeneity in and between cell populations. Pseudotime analysis visualized haematopoietic stem (HSC) to progenitor transitions, identified HSC as well as lineage-specific transcriptional programs, and also highlighted putative lineage branching points. To provide access to the wider scientific community, a user-friendly website was developed with intuitive search and display functionality.

Dataset features

Information

Specifications

Application:	RNA-seq analysis
Number of samples:	3840
Release date:	Jul 4 2016
Last update date:	Nov 26 2018
Access:	Public
Taxon:	Mus musculus
Dataset link	The transcriptional landscape of mouse blood stem/progenitor cell transitions at single cell resolution

Experimental Protocol

Single cell RNA sequencing of haematopoeitic stem and progenitor cells

Repositories

GEO

ArrayExpress

ENA

BioProject

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Contact

Evangelia Diamanti