BoneMarrowMap: A Balanced Single-cell Reference Atlas of Human Hematopoiesis

We provide a large-scale reference atlas of human hematopoiesis with balanced representation of CD34+ stem and progenitor cells together with terminally differentiated populations. Our reference map of 263,159 hematopoietic cells provides us with deep portraits of lineage transitions in both early and late stages of human hematopoiesis.

HSPC annotations within this atlas were carefully validated to maximize concordance with immunophenotypically pure populations established through decades of functional studies. In particular, our transcriptionally defined HSC state is highly concordant with immunophenotypically defined Lin-CD34+CD38-CD45RA-CD90+CD49f+ long-term HSCs.

Please visit the Github page for our R package to access functions for mapping query scRNA-seq profiles of normal or leukemic hematopoietic cells onto BoneMarrowMap. The entire process is optimized to take <10 min total for mapping ~100,000 single cells on a personal laptop.

See also our Blood Cancer Discovery publication (Zeng et al, 2025) for more details on the atlas and an example of its application to leukemia.