ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR321/094/SRR32117594/SRR32117594_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR321/098/SRR32117598/SRR32117598_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR321/096/SRR32117596/SRR32117596_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR321/095/SRR32117595/SRR32117595_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR321/094/SRR32117594/SRR32117594_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR321/000/SRR32117600/SRR32117600_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR321/093/SRR32117593/SRR32117593_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR321/097/SRR32117597/SRR32117597_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR321/097/SRR32117597/SRR32117597_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR321/099/SRR32117599/SRR32117599_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR321/000/SRR32117600/SRR32117600_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR321/099/SRR32117599/SRR32117599_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR321/098/SRR32117598/SRR32117598_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR321/096/SRR32117596/SRR32117596_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR321/095/SRR32117595/SRR32117595_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR321/093/SRR32117593/SRR32117593_2.fastq.gzprimaryOK200GenomicsNankai Universityhttps://www.ebi.ac.uk/ena/browser/view/PRJNA1215379Mus musculusCD11b+ cell populations, especially macrophages, are highly heterogeneous tissue-resident immune cells in mice and humans. The exact subpopulation and its phenotype remain unknown. Here, we analyzed intestinal CD11b+ cell populations from normal and Runx3 macrophage conditionally deficient mice using scRNA-seq. We found that the transcription factor RUNX3 plays a key role in the entry of inflammatory monocytes into resident macrophages. Decreased resident macrophages and elevated ZFP36 in RUNX3flow/flowlyz2-Cre mice, leading to cytokine and chemokine degradation in colon tissue-resident macrophages. RUNX3 promotes the expression of NR4A1, thereby inducing the differentiation of inflammatory monocytes into resident macrophages. Single-cell population analysis revealed that the ERK1/2/MAPK pathway plays a key role in NR4A1-mediated gut-resident macrophage differentiation. Overall design: 10X Genomics scRNA-seq was performed to better assess immune cell heterogeneity in gut lamina propria (LP).ENAfalseSingle-cell RNA sequencing revealed the transcriptional landscape and heterogeneity of macrophages in the intestinal tissues of WT and RUNX3 macrophage conditional knockout mice.Single-cell RNA sequencing revealed the transcriptional landscape and heterogeneity of macrophages in the intestinal tissues of WT and RUNX3 macrophage conditional knockout mice.2025-09-242025-01-30PRJNA1215379GSE28797010090