{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Bert Malengier"],"organism":["Mus musculus"],"software":["Cell Ranger","Cell Ranger, Seurat"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17170"],"description":["Synovial joints harbor a protective lining layer, consisting of fibroblasts and macrophages, which form an epithelial-like barrier. In inflamed joints, lining macrophages regulate both early inflammatory cell influx and resolution. Despite these critical functions, it is currently unknown at what stage during development the synovial macrophage lining is established, and which signals drive this process."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - GEX libraries and CMO libraries were pooled together with PhiX Control v3 (~1%) and sequenced on the NextSeq 2000 platform or the NovaSeq 6000 platform using the NextSeq 1000/2000 P3 Reagents (100 cycles) v3 Kit or the NovaSeq 6000 S2 Reagent (100 cycles) Kit v1.5 following a paired-end reading strategy. Sequencing of the single cell libraries was performed by Edinburgh Genomics and the Edinburgh Genetics Core.","Sample Collection - Synovial cells were isolated followed by cell sorting through a 70-μm nozzle using the Fusion Q cell sorter. Prior to sorting, DAPI (4′,6-diamidino-2-phenylindole) (Thermo Fisher) was added to the cell suspension to exclude dead cells. Sorted populations included non-neutrophil immune cells (DAPI- CD45+ Ly6G-) and fibroblasts/endothelial cells (DAPI- CD45- CD31+ or Podoplanin+). Post-sort cell count showed that all sorted populations exhibited a viability exceeding 90%. Before loading cells sorted cells to the 10X platform, the immune cells were pooled with the sorted fibroblasts/endothelial cells.","Library Construction - GEX and CMO libraries were purified using SPRIselect beads (Beckman Coulter). The libraries were quantified and assessed for size distribution on the Qubit 2.0 Fluorometer (Thermo Fisher) and the Agilent Bioanalyzer (Agilent Technologies) using the Qubit dsDNA HS assay Kit and the DNA HS Kit, respectively. Results were utilized to calculate the library molarity. Library preparation and quality control were conducted at the IRR Cell Sorting Facility.","Nucleic Acid Extraction - Gene expression (GEX) and multiplex (CMO) libraries were generated using the Chromium Single Cell 3' Reagent Kit V3.1 from 10X Genomics following the manufacturer’s instructions. Each sample loaded onto a 10X Genomics cartridge consisted of up to 60,000 cells. Different litters or sexes were pooled before sorting using the 3’ CellPlex Kit Set A, following the manufacturer’s instructions (10X Genomics)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Reads were converted to the fastq format using the Cell Ranger mkfastq pipeline (10X Genomics, V7.1.0). Before alignment, the STAR indexes for read alignment were built by combining the mouse reference genome (GRCm38) with the corresponding genomic sequence of Cre, GFP, tdTomato.","Data Transformation - Raw gene expression matrices were generated and demultiplexed per sample using the Cell Ranger multi-pipeline (10X Genomics, V7.1.0). Individual raw gene expression matrices per sample were merged and analyzed using the Seurat package. The cell matrices underwent filtering, removing cell barcodes with < 200 features, >5101 features (95th percentile cutoff), >18801 expressed genes (95th percentile cutoff), or >7.5% of reads mapped to mitochondrial RNA. The remaining cells were normalized using the LogNormalize method, and the 3000 most variable genes were selected for principal component analysis (PCA) to reduce dimensionality and cluster all cell types. The selection of principal components was based on elbow and Jackstraw plots (typically 40–50). Harmony, with a theta value of 0, was applied to correct for different sample lanes. After quality filtering, we obtained ~630 million unique transcripts from 60,929 cells, each with more than 200 genes, averaging 3,160 genes per cell. This included 13,050 (21.4%), 11,961 (19.6%), 13,876 (22.8%), and 22,042 (36.2%) cells from newborns (NB), 1-week-old, 3-week-old, and adult mice, respectively."],"omics_type":["Unknown","Transcriptomics"],"instrument_platform":["NextSeq 2000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"pubmed_title":["Synovial lining macrophages form during early postnatal life via fetal-derived CX3CR1+ cells and AQP1+ intermediates"],"pubmed_authors":["Marléne Magalhaes Pinto, Bert Malengier-Devlies, Guillaume Seuzaret, Anna Ahlback,  Solvig Becker, Katelyn Patatsos, Georgios Drakoulis, Julia Karjalainen, Christiane Ruedl,  David Voehringer, Calum C Bain, Elaine Emmerson, Barbora Schonfeldova, Kristina Zec,  Irina Udalova, Theodoros Simakou, Lucy MacDonald, Mariola Kurowska-Stolarska,  Jadwiga Miotla-Zarebska, Tonia Vincent, Romeo Ricci, Eric Erbs, Jack Barrington,  Barry W McColl, Georgiana Neag, Christopher Mahony, Adam P Croft, Louis Boon,  Matthieu Vermeren, Marc Bajénoff, Oumaima Ben Brahim, Stefan Uderhardt,  Alexandre Gallerand, Stoyan Ivanov, Rebecca Gentek","Rebecca Gentek","Bert Malengier"],"additional_accession":[]},"is_claimable":false,"name":"Single-Cell RNA Sequencing of Mouse Synovial Tissue Across Developmental Time Points","description":"Synovial joints harbor a protective lining layer, consisting of fibroblasts and macrophages, which form an epithelial-like barrier. In inflamed joints, lining macrophages regulate both early inflammatory cell influx and resolution. Despite these critical functions, it is currently unknown at what stage during development the synovial macrophage lining is established, and which signals drive this process.","dates":{"release":"2026-06-09T00:00:00Z","modification":"2026-06-16T16:40:25.785Z","creation":"2026-06-16T16:39:14.592Z"},"accession":"E-MTAB-17170","cross_references":{"ENA":["ERP195211"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}