{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Julian Hofmann"],"organism":["Mus musculus"],"software":["10X Genomics Cell Ranger"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15320"],"description":["Immune cells were isolated from hematopoietic and non-hematopoietic tissues from fetal and newborn mice and analyzed by scRNA-sequencing."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Single-cell RNA-sequencing libraries were prepared according to the manufacturer’s instructions (CG00052 RevB) using 10X Genomics Chromium Single Cell 30 Library and Gel Bead Kit v3 and Chromium Single Cell A Chip Kit.","Sample Treatment - If no treatment is specified, samples were collected from embryos or newborn mice in steady state conditions. For embryonic dexamethasone treatment or LPS exposure experiments, pregnant dams at E17.5 were injected i.p. with either 5 mg/kg of dexamethasone (D2915, Sigma-Aldrich) in PBS or 100 µg/kg LPS (from E. coli O55:B5; L4524, Sigma-Aldrich) in 0.9% (w/v) NaCl solution or the equivalent volume of the respective solvent. Animals were euthanized 2 or 4 hours after dexamethasone or LPS treatment, respectively, as described above.","Sample Collection - Blood was collected by bleeding into heparin-Phosphate Buffered Saline (PBS; D8537, Sigma-Aldrich; 50 µl of 100 IU/ml heparin (585661, LEO Pharma) in 500 µl of PBS) from euthanized E17.5 and newborn mice. Testes, kidneys, and liver were gently minced with scissors and digested with 50 µg/ml DNase 1 (10104159001, Roche) and 1 mg/ml Collagenase D (11088866001, Roche) in Hank’s Buffered Saline (HBSS; RNBF2378, Sigma-Aldrich) solution at 37 °C for 15 to 45 min. Bone marrow cells were collected by carefully crushing and rinsing the femora (and from embryos also tibiae) with HBSS, followed by sequential filtering through silk cloth (pore size 77 µm, 77-48Y115, Marabu Scandinavia) until no visible aggregates were detected. Finally, all isolated cells were washed with 500 µl of PBS and suspended in PBS and filtered through a silk cloth.  Cells were stained for flow cytometry without fixation and sorted with a Sony SH800 Cell Sorter (100 µm nozzle, purity mode). Single cells were gated with FSC-H vs. FSC-W and SSC-H vs. SSC-W to avoid doublets, and dead cells were excluded. Live single CD45+ cells (kidney, testis) or CD45+ CD3- CD45R- cells (liver, BM, blood) were sorted into the RPMI-1640 medium containing 2% (v/v) FCS. Freshly sorted CD45+ cells were processed immediately according to 10X Genomics guidelines (CG000126_Guidelines for Optimal Sample Prep Flow Chart RevA).","Nucleic Acid Extraction - Single-cell RNA-sequencing libraries were prepared according to the manufacturer’s instructions (CG00052 RevB) using 10X Genomics Chromium Single Cell 30 Library and Gel Bead Kit v3 and Chromium Single Cell A Chip Kit.","Sequencing - The libraries were sequenced using the Illumina Novaseq6000 Sequencing System (RRID: SCR_016387)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - The Cell Ranger (ver. 7.1.0 or 7.0.1, 10X Genomics) \\\"count\\\" function was used to align samples to the mm10-2020-A reference genome, quantify reads, and filter reads and barcodes.","Data Transformation - The Cell Ranger (ver. 7.1.0 or 7.0.1, 10X Genomics) \\\"count\\\" function was used to align samples to the mm10-2020-A reference genome, quantify reads, and filter reads and barcodes."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"pubmed_abstract":["Development 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."],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"pubmed_title":["Tissue-resident neutrophils serve homeostatic and immunological functions in embryos"],"pubmed_authors":["Julian Hofmann","Julian Hofmann,  Laura Lintukorpi,  Emmi Lokka, Venla Ojasalo,  Venla Korpela, Sheyla Cisneros Montalvo, Damien Kaukonen,  Lin Ma,  Noora Kotaja,  Heidi Gerke,  Marko Salmi,  Pia Rantakari","Pia Rantakari"],"additional_accession":[]},"is_claimable":false,"name":"scRNA-sequencing of embryonic and neonatal immune cells isolated from various organs","description":"Immune cells were isolated from hematopoietic and non-hematopoietic tissues from fetal and newborn mice and analyzed by scRNA-sequencing.","dates":{"release":"2026-06-09T00:00:00Z","modification":"2026-06-09T12:48:02.528Z","creation":"2025-07-04T12:33:00.635Z"},"accession":"E-MTAB-15320","cross_references":{"ENA":["ERP174658"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003969","EFO_0004184"],"doi":["10.1101/2025.06.12.659311"]}}