Galaxy-compatible AnnData object for pseudobulk analysis

This dataset is an AnnData object containing a curated subset of single-cell RNA-seq data. It includes non-classical monocytes (NCMs) and plasmacytoid dendritic cells (pDCs) derived from both bone marrow and peripheral blood samples.

The dataset has been preprocessed and annotated with the metadata required for pseudobulk analysis, including cell type labels, condition, batch information, and tissue of origin.

This subset has been prepared for educational purposes and is used to demonstrate pseudobulk aggregation and differential expression analysis in the Galaxy platform.

A portion of the bone marrow data originates from the following publication:

Rettkowski J, Romero-Mulero MC, Singh I, Wadle C, Wrobel J, Chiang D, Hoppe N, Mess J, Schönberger K, Lalioti ME, Jäcklein K, SilvaRego B, Bühler T, Karabacz N, Egg M, Demollin H, Obier N, Zhang YW, Jülicher C, Hetkamp A, Czerny M, Jones MJ, Seung H, Jain R, von Zur Mühlen C, Maier A, Lother A, Hilgendorf I, van Galen P, Kreso A, Westermann D, Rodriguez-Fraticelli AE, Heidt T, Cabezas-Wallscheid N.
"Modulation of bone marrow haematopoietic stem cell activity as a therapeutic strategy after myocardial infarction: a preclinical study."
Nature Cell Biology. 2025 Apr;27(4):591–604.
doi: 10.1038/s41556-025-01639-4
PMID: 40175666 ; PMCID: PMC11991920