Short-read and long-read RNA sequencing of mouse hematopoietic stem cells at bulk and single-cell levels

Xiuran Zheng,Li Chen,Dan Zhang,Yiming Zhang,Mengying Xu,Lu Chen,Jing-Wen Lin,Wanqin Zeng,Chao Tang,Ran Zhou

doi:10.1038/s41597-021-01078-4

Abstract

Hematopoietic stem cells (HSCs) lie at the top of the differentiation hierarchy. Although HSC and their immediate downstream, multipotent progenitors (MPP) have full multilineage differentiation capacity, only long-term (LT-) HSC has the capacity of long-term self-renewal. The heterogeneity within the HSC population is gradually acknowledged with the development of single-cell RNA sequencing and lineage tracing technologies. Transcriptional and post-transcriptional regulations play important roles in controlling the differentiation and self-renewal capacity within HSC population. Here we report a dataset comprising short- and long-read RNA sequencing for mouse long- and short-term HSC and MPP at bulk and single-cell levels. We demonstrate that integrating short- and long-read sequencing can facilitate the identification and quantification of known and unannotated isoforms. Thus, this dataset provides a groundwork for comprehensive and comparative studies on transcriptional diversity and heterogeneity within different HSC cell types.

Highlights

Hematopoiesis starts with a population of self-renewing hematopoietic stem cells (HSCs), which produce a series of increasingly more lineage-committed progenitor cells, giving rise to all types of mature blood cells
Similar to the single-cell data, ST-HSC lied in between LT-HSC and multipotent progenitors (MPP), corresponding to their biological status. These results showed that the cells were correctly sorted and both the bulk and single-cell short-read RNA sequencing (RNA-seq) data were of high quality
The Principal component analysis (PCA) illustrated that the samples were clustered by cell type between short-read and long-read sequencing replicates after batch correction (Fig. 4f). These results suggested that long-read sequencing data were of high quality, and the biological replicates are of high concordance

Summary

Introduction

Background & SummaryHematopoiesis starts with a population of self-renewing hematopoietic stem cells (HSCs), which produce a series of increasingly more lineage-committed progenitor cells, giving rise to all types of mature blood cells. We present comprehensive transcriptomic profiling of mouse HSC and MPP using both short-read and long-read RNA sequencing at bulk and single-cell levels. For single-cell sequencing data, we examined the proportion of reads mapped to mitochondrial and ribosomal genes (Fig. 2d).

Results

Conclusion