biostudies-arrayexpressJulian HofmannMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15317Embryonic (E17.5) testes and kidneys from wildtype or Gfi1[R412X] mice, a model of severe congenital neutropenia, were analyzed by bulk RNA-sequencing.biostudies-arrayexpressLibrary Construction - Sample quality was assessed using an Agilent Advanced Analytical Fragment Analyzer and Stranded mRNA Library Preparation (1000000124518, Illumina) was performed.Sequencing - Next-generation sequencing performed by the Finnish Functional Genome Centre (Turku Bioscience Centre, Finland) using an Illumina NovaSeq 6000 SP v1.5 (650–800 M reads/run, 2 lanes).Nucleic Acid Extraction - RNA was isolated with either the NucleoSpin RNA, Mini kit for RNA purification (kidneys) or RNeasy Plus Micro Kit (testes, 74034, Qiagen) according to the manufacturer’s protocol.Sample Collection - Kidneys (both) and testes (both) from male WT and Gfi1mut/mut E17.5 embryos were collected in RNAlater RNA Stabilization Reagent and stored frozen until processing.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Transcript assembly was done using stringtie (ver. 2.2.1) and the read count matrix was prepared using the prepDE.py3 script provided with HiSAT2.Sequence Alignment - Quality of the reads was assessed using FASTQC (ver. 0.12.1), reads were trimmed using BBMap (ver. 39.06) and aligned to the GRCm38.84 genome using HiSAT2 (ver. 2.2.1). Reads were then sorted by coordinate and filtered by alignment score using a cutoff of greater than 30 using samtools (ver. 1.19.2).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000Development of neutrophils in the bone marrow and their crucial role in first-line defense are well understood in adults, but remarkably little is known about fetal neutrophils. Here, we analyzed the production, distribution, and functions of neutrophils during embryonic development in the mouse. We discovered that multiple non-hematopoietic steady-state organs harbor substantial numbers of immature and mature neutrophils, many of which are localized to tissue parenchyma outside the vessels. Using single-cell transcriptomic analyses, we revealed the presence of neutrophil progenitors and precursor cells in the blood and even in non-hematopoietic tissues in fetal and newborn mice. Embryonic tissue-resident neutrophils were transcriptionally different from embryonic blood-borne neutrophils and adult neutrophils. We demonstrated, through functional analyses, that embryonic neutrophils proliferated actively, had a high glycolytic capacity, and exhibited distinct diurnal rhythmicity. Embryonic neutrophils displayed lineage-specific innate immune effector functions and were responsive to maternal immunostimulation and immunosuppression. Using a genetic embryonic neutrophil depletion model, we discovered that neutrophils impact the piRNA pathway in the testis. Collectively, our data provides an atlas of the fetal neutrophil landscape and dissects their responses in steady-state. <h4>Summary</h4> Non-hematopoietic steady-state tissues harbor extravascular immature and mature neutrophils during fetal development. Embryonic neutrophils are endowed with multiple effector mechanisms and also serve homeostatic roles during tissue development.RNA-seq of coding RNAMus musculusTissue-resident neutrophils serve homeostatic and immunological functions in embryosJulian HofmannJulian Hofmann, Laura Lintukorpi, Emmi Lokka, Venla Ojasalo, Venla Korpela, Sheyla Cisneros Montalvo, Damien Kaukonen, Lin Ma, Noora Kotaja, Heidi Gerke, Marko Salmi, Pia RantakariPia RantakarifalseBulk RNA-sequencing of testes and kidneys from wildtype and Gfi1[R412X] embryonic miceEmbryonic (E17.5) testes and kidneys from wildtype or Gfi1[R412X] mice, a model of severe congenital neutropenia, were analyzed by bulk RNA-sequencing.2026-06-09T00:00:00Z2026-06-09T12:47:14.859Z2025-07-03T17:38:48.364ZE-MTAB-15317ERP174617EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_000418410.1101/2025.06.12.659311