NicheScribe: consistent and generalizable annotation of stromal cells in the murine bone marrow niche
- 1Columbia University Irving Medical Center
Abstract
Hematopoietic stem and progenitor cells (HSPC) depend on interactions with nearby stromal cells to support their homeostatic functions and mount responses to perturbations. The murine bone marrow (BM) niche can be profiled using single-cell RNA sequencing (scRNA-seq), but there is considerable inconsistency in cell type identification, and uncertainty over how populations can be isolated prospectively by flow cytometry. Here, we produced new scRNA-seq reference datasets using purified populations of murine BM stromal cells, which we used to create a bespoke classifier for stromal cells. Our NicheScribe approach is consistent, accurate, and generalizable to query datasets irrespective of methods used for cell isolation. Moreover, consistent annotation permits comparative analyses of the same stromal cells across different bone types and perturbations like inflammation, neoplasia, and aging. Our work provides new tools for consistent cell type annotation in the murine BM niche and new insights for combined molecular and functional analyses.
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BibTeX
@misc{swann2026nichescribe,
title = {{NicheScribe: consistent and generalizable annotation of stromal cells in the murine bone marrow niche}},
author = {J. W. Swann and J. H. Fung and R. Zhang and R. Rabadan and E. Passegue},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.23.753907},
url = {https://www.biorxiv.org/content/10.64898/2026.09.23.753907v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - NicheScribe: consistent and generalizable annotation of stromal cells in the murine bone marrow niche
AU - J. W. Swann
AU - J. H. Fung
AU - R. Zhang
AU - R. Rabadan
AU - E. Passegue
PY - 2026
DA - 2026/09/23
PB - bioRxiv
DO - 10.64898/2026.09.23.753907
UR - https://www.biorxiv.org/content/10.64898/2026.09.23.753907v1
AB - Hematopoietic stem and progenitor cells (HSPC) depend on interactions with nearby stromal cells to support their homeostatic functions and mount responses to perturbations. The murine bone marrow (BM) niche can be profiled using single-cell RNA sequencing (scRNA-seq), but there is considerable inconsistency in cell type identification, and uncertainty over how populations can be isolated prospectively by flow cytometry. Here, we produced new scRNA-seq reference datasets using purified populations of murine BM stromal cells, which we used to create a bespoke classifier for stromal cells. Our NicheScribe approach is consistent, accurate, and generalizable to query datasets irrespective of methods used for cell isolation. Moreover, consistent annotation permits comparative analyses of the same stromal cells across different bone types and perturbations like inflammation, neoplasia, and aging. Our work provides new tools for consistent cell type annotation in the murine BM niche and new insights for combined molecular and functional analyses.
ER -