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Transcriptomic characterisation of haematopoietic stem and progenitor cells from human adult bone marrow, spleen and peripheral blood

Updated September 30, 2021

Haematopoietic stem and progenitor cells (HSPCs), the precursors of all blood cells, reside predominantly in the bone marrow (BM). Recent evidence suggests that other anatomical sites may contribute significantly to blood production, but the cellular, molecular and functional composition of extramedullary HSPC pools remains unexplored. Here, we comprehensively characterized the single-cell composition of the adult human HSPC pool within paired BM, spleen and peripheral blood (PB) from two healthy organ donors. 10x scRNA-seq of 30000 HSPCs from all three sites defined transcriptionally distinct cell clusters that correspond to precursors of all haematopoietic lineages but also stem cells (HSCs). Although most clusters were common to all organs, their proportions significantly differed between tissues. Altogether our data provides evidence that different organs sustain distinct topologies of the hematopoietic hierarchy, originating from HSC subsets with distinct lineage preferences. This dataset is part of the Human Cell Atlas.

Elisa LaurentiWellcome - MRC Cambridge Stem Cell Instituteel422@cam.ac.uk
Hugo P BastosWellcome - MRC Cambridge Stem Cell Institutehpb29@cam.ac.uk
Elisa Laurenti (Principal Investigator)1
Kourosh Saeb-Parsy (Principal Investigator)2
Hugo P Bastos (Computational Scientist)1
Nicole Mende (Experimental Scientist)1
Krishnaa Mahbubani (Experimental Scientist)2
Abbie Curd (Experimental Scientist)2
1Wellcome - MRC Cambridge Stem Cell Institute
2University of Cambridge
Ray Stefancsik

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Analysis Portals


Project Label



Homo sapiens

Sample Type


Anatomical Entity

3 anatomical entities

Organ Part


Selected Cell Types

3 cell types

Disease Status (Specimen)


Disease Status (Donor)

2 disease statuses

Development Stage

human adult stage

Library Construction Method

3 library construction methods

Nucleic Acid Source

single cell

Paired End


File Format

4 file formats

Cell Count Estimate


Donor Count

bam32 file(s)fastq.gz336 file(s)h5ad1 file(s)loom35 file(s)