scRNA-seq data for article: Kupffer cell and recruited macrophage heterogeneity orchestrate granuloma maturation and hepatic immunity in visceral leishmaniasis

Single-cell RNA-seq dataset from sorted CD11bInt, F4/80Hi, CD64+ mouse liver cells in naive or Leishmania infantum-infected animals at 42 d.p.i.. Data analyses and results are described in manuscript: "Kupffer cell and recruited macrophage heterogeneity orchestrate granuloma maturation and hepatic immunity in visceral leishmaniasis". Data files are Seurat objects in RDS format. Filtered-out potential doublets, low quality cells and dying cells (excluded cells with <1000 genes detected, cells with >6000 genes detected, cells with mitochondrial gene expression > 10% and cells with <5000 transcript molecules). Data normalization, scaling and integration performed using Seurat.

Filtered dataset containing all KCs and macrophages is in the "pessenda_KC_Macro_seurat" file.

Our data were then mapped onto a reference dataset published by Remmerie et al. (DOI: 10.1016/j.immuni.2020.08.004) for annotation consistent with the literature. The reference mapped object can be found in the "pessenda_refmap_KC_Macro_seurat" file.

Dataset containing the additional analysis of CLEC4F-TIM4+ FACS-sorted KCs can be found in the "pessenda_refmap_KCTimPos_seurat" file.