An integrated analysis of human myeloid cells identifies gaps in in vitro models of in vivo biology

Nadia Rajab, Paul W Angel, Yidi Deng, Jennifer Gu, Vanta Jameson, Mariola Kurowska-Stolarska, Simon Milling, Chris M Pacheco, Matt Rutar, Andrew L Laslett, Kim-Anh Lê Cao, Jarny Choi, Christine A Wells

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)
52 Downloads (Pure)


The Stemformatics myeloid atlas is an integrated transcriptome atlas of human macrophages and dendritic cells that systematically compares freshly isolated tissue-resident, cultured, and pluripotent stem cell-derived myeloid cells. Three classes of tissue-resident macrophage were identified: Kupffer cells and microglia; monocyte-associated; and tumor-associated macrophages. Culture had a major impact on all primary cell phenotypes. Pluripotent stem cell-derived macrophages were characterized by atypical expression of collagen and a highly efferocytotic phenotype. Myeloid subsets, and phenotypes associated with derivation, were reproducible across experimental series including data projected from single-cell studies, demonstrating that the atlas provides a robust reference for myeloid phenotypes. Implementation in allows users to visualize patterns of sample grouping or gene expression for user-selected conditions and supports temporary upload of your own microarray or RNA sequencing samples, including single-cell data, to benchmark against the atlas.

Original languageEnglish
Pages (from-to)1629-1643
Number of pages15
JournalStem Cell Reports
Issue number6
Publication statusPublished - 8 Jun 2021


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