biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsMechthild LütgeIllumina NovaSeq 6000RNA-seq of coding RNA from single cellsMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13891Lymph nodes (LNs) are essential hubs for the induction and regulation of immune responses. Immune activation, either systemic or local, is accompanied by the lymph node swelling response, which results in up to threefold expansion in volume. Increased immigration of immune cells via the blood vasculature causes the LN swelling response with retention of lymphocytes and myeloid cells in perivascular niches. The perivascular niche is supported by fibroblastic cells known as mural cells (vascular smooth muscle cells (VSMCs) and pericytes) and by perivascular reticular cells (PRCs) that connect the perivascular niche to the fibroblastic reticular cell (FRC) network. Here, we used high-resolution confocal microscopy, flow cytometry, single cell transcriptomics and cell fate mapping in mouse models to delineate VSMC and PRC phenotypes and differentiation during development in different LN entities.biostudies-arrayexpressSample Collection - For stromal cell isolation from peripheral (inguinal, brachial and axillary) and mesenteric lymph nodes, tissues were disrupted into small pieces using small needles and collected in RPMI 1640 medium containing 2% FCS, 20 mM HEPES pH 7.2 (Lonza), 0.16 mg/ml collagenase P, Dispase 30 μg/ml (Roche) and 25 μg/ml DNase I. The dissociated tissue was incubated for 45 min at 37 °C, during the incubation time the tissue was resuspended and supernatant was collected every 15 min.Nucleic Acid Extraction - Enrichment of stromal cells was performed by incubating the cell suspension with MACS anti-CD45 and anti-TER119 microbeads (Miltenyi Biotec) and passing it through MACS LS columns (Miltenyi Biotec). Single-cell suspensions were stained for further cell sorting. Stromal cells were sorted for CD31-EYFP+ cells and were filled up with CD31-EYFP- cells. Cell sorting was performed using a BD FACSMelody Cell Sorter and the FACSChorus (v.1.3) software (BD Biosciences).Sequencing - Libraries were sequenced via NovaSeq 6000 Illumina sequencing at the Functional Genomics Center ZurichLibrary Construction - cDNA library generation was performed following the established commercial protocol for Chromium Single Cell 3’ Reagent Kit (v3 Chemistry).OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesMechthild LütgefalseSingle cell RNAseq of fibroblastic reticular cells from mesenteric and inguinal murine lymph nodes at different developmental stagesLymph nodes (LNs) are essential hubs for the induction and regulation of immune responses. Immune activation, either systemic or local, is accompanied by the lymph node swelling response, which results in up to threefold expansion in volume. Increased immigration of immune cells via the blood vasculature causes the LN swelling response with retention of lymphocytes and myeloid cells in perivascular niches. The perivascular niche is supported by fibroblastic cells known as mural cells (vascular smooth muscle cells (VSMCs) and pericytes) and by perivascular reticular cells (PRCs) that connect the perivascular niche to the fibroblastic reticular cell (FRC) network. Here, we used high-resolution confocal microscopy, flow cytometry, single cell transcriptomics and cell fate mapping in mouse models to delineate VSMC and PRC phenotypes and differentiation during development in different LN entities.2025-11-11T00:00:00Z2025-11-11T21:49:42.715Z2025-11-11T14:11:14.473ZE-MTAB-13891ERP158395EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0004184