Fetal liver macrophages contribute to the hematopoietic stem cell niche by controlling granulopoiesis

During embryogenesis, the fetal liver becomes the main hematopoietic organ, where stem and progenitor cells as well as immature and mature immune cells form an intricate cellular network. Hematopoietic stem cells (HSCs) reside in a specialized niche, which is essential for their proliferation and differentiation. However, the cellular and molecular determinants contributing to this fetal HSC niche remain largely unknown. Macrophages are the first differentiated hematopoietic cells found in the developing liver, where they are important for fetal erythropoiesis by promoting erythrocyte maturation and phagocytosing expelled nuclei. Yet, whether macrophages play a role in fetal hematopoiesis beyond serving as a niche for maturing erythroblasts remains elusive. Here, we investigate the heterogeneity of macrophage populations in the fetal liver to define their specific roles during hematopoiesis. Using a single-cell omics approach combined with spatial proteomics and genetic fate-mapping mod..., 5µm slices of fetal liver from E14.5 wildtype embryos were prepared and used for CODEX staining following the manufacturer’s instructions. Briefly, sections were retrieved from the freezer, let dry on drierite beads, and fixed for 10 min in ice-cold acetone (Sigma Aldrich, St. Louis, MO, USA). After fixation, samples were rehydrated and photobleached twice as described in (Du, Lin et al. 2019). Following photobleaching, sections were blocked and stained with a 20-plex CODEX antibody panel (Table S5 and S6) overnight at 4 Â°C. After staining, samples were washed, fixed with ice-cold methanol, washed with 1x PBS, and fixed for 20 min with BS3 fixative (Sigma Aldrich, St. Louis, MO, USA). A final washing step with 1x PBS was performed.
A multicycle CODEX experiment was performed following the manufacturer’s instructions. Images were acquired with a Zeiss Axio Observer widefield fluorescence microscope using a 20x objective (NA 0.85) and z-spacing of 1.5µm. The 405, 488, 568, and 647 nm..., , # Data from: Fetal liver macrophage imaging and transcriptomic datasets

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This dataset accompanies the article *“Fetal liver macrophages contribute to the hematopoietic stem cell niche by controlling granulopoiesis”* (Kayvanjoo et al., eLife 2024). It brings together multiplexed tissue imaging (CODEX) of mouse fetal liver at embryonic day (E)14.5 and quantitative source data for the main figures. The data capture the spatial distribution and phenotypic heterogeneity of fetal liver macrophage subpopulations, their physical proximity to long‑term hematopoietic stem cells (LT‑HSCs), and downstream effects on erythropoiesis and granulopoiesis.

The Dryad record contains the raw CODEX image data and associated analytical outputs. RNA‑seq data from bulk and single‑cell experiments are hosted separately at GEO (GSE225444) and are referenced here so that users can combine imaging, flow‑cytometry and transcriptomic layers wh...,