Single-cell gene expression profiles of GM-CSF cultured bone marrow cells treated with HCQ or cGAMP.

We performed single-cell RNA sequencing (scRNA-seq) of granulocyte-macrophage colony-stimulating factor (GM-CSF) cultured bone marrow cells (GM-BMCs) treated with hydroxychloroquine (HCQ) or cyclic guanosine monophosphate–adenosine monophosphate (cGAMP) to reveal a divergence of the gene expression pattern in interferon ß (IFNß)-expressing cells between HCQ and cGAMP treatments. Overall design: Bone marrow cells were isolated from the legs of mice and cultured in RPMI 1640 (Nacalai Tesque, Kyoto, Japan) containing 10% foetal bovine serum (FBS) (Sigma-Aldrich, St. Louis, MO, USA) and 10 ng/ml of GM-CSF (PeproTech, Cranbury, NJ, USA). Red blood cells (RBCs) were lysed with RBC lysis buffer (Thermo Fisher Scientific, Waltham, MA, USA) before culture. After 4 days, additional GM-CSF (10 ng/ml) was added and used for the experiment on days 6–7. GM-BMCs were treated with HCQ (100 µM) or cGAMP (5 µg/ml) for 6 h and subjected to scRNA-seq analysis.