{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Lisa Kurz"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15366"],"description":["The interaction of immune cells in the lymph node microenvironment depends on the infrastructure and molecular cues provided by fibroblastic reticular cells (FRCs). In addition, concentric layers of still poorly defined mural cells, including vascular smooth muscle cells (VSMCs), are involved in positioning and regulating immune cell interactions. Here, we used high-resolution confocal microscopy, flow cytometry, single cell transcriptomics and trajectory analysis to delineate VSMC and PRC phenotypes and differentiation during development in different LN entities."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - cDNA library generation was performed following the established commercial protocol for Chromium Single Cell 3’ Reagent Kit (v3.1 Chemistry).","Sample 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 Zurich"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Lisa Kurz"],"additional_accession":[]},"is_claimable":false,"name":"Single cell RNAseq of fibroblastic reticular cells and vascular smooth muscle cells from mesenteric and peripheral murine lymph nodes at different developmental stages","description":"The interaction of immune cells in the lymph node microenvironment depends on the infrastructure and molecular cues provided by fibroblastic reticular cells (FRCs). In addition, concentric layers of still poorly defined mural cells, including vascular smooth muscle cells (VSMCs), are involved in positioning and regulating immune cell interactions. Here, we used high-resolution confocal microscopy, flow cytometry, single cell transcriptomics and trajectory analysis to delineate VSMC and PRC phenotypes and differentiation during development in different LN entities.","dates":{"release":"2025-09-01T00:00:00Z","modification":"2025-09-01T01:02:28.019Z","creation":"2025-07-20T22:11:18.513Z"},"accession":"E-MTAB-15366","cross_references":{"ENA":["ERP176959"],"Biostudies":["E-MTAB-13891"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0004184"]}}