{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Robert Rusch"],"instrument_platform":["10x Genomics Chromium Controller","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-16511"],"description":["This dataset contains single-cell RNA-seq profiles generated to investigate the phenotypic plasticity of mesenchymal stem/stromal cells (MSCs), with a focus on freshly isolated murine CD45-, TER119-, Sca-1+, PDGFRα+ (PαS) cells. Following transplantation into irradiated recipients, a subset of PαS cells acquired macrophage-like features, expressing CD45, CD68, and CSF1R/CD115. In vitro culture of PαS cells in macrophage differentiation media induced an M2-like signature (CD45, CD68, CD206) via CSF1R-dependent pathways. The dataset includes murine MSC samples from the C57/BL6 strain. The sequencing data support the identification of macrophage-like transcriptional clusters within the PαS population."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Freshly isolated PαS cells were plated and cultured in either DMEM or RM for 1 week as described in the manuscript. After culture, cells were washed twice with PBS and dissociated into single cells. Approximately 10,000 viable cells per sample were prepared for loading onto the Chromium Controller (10x Genomics).","Sequencing - Sequencing was performed on an Illumina NovaSeq 6000 platform (Illumina). Raw sequencing data were processed using Cell Ranger software to generate filtered feature-barcode matrices.","Library Construction - Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ Reagent Kits v3.1 (Dual Index, 10x Genomics) according to the manufacturer’s instructions (v3.1 Chemistry Dual Index).","Nucleic Acid Extraction - Single-cell suspensions were directly processed according to the Chromium Single Cell 3′ Reagent Kits v3.1 workflow (10x Genomics), in which RNA capture and cDNA synthesis occur during single-cell encapsulation and barcoding within the Chromium system."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Satoru Morikawa","Yoko Ogawa","Shigeto Shimmura","Yo Mabuchi","Robert Rusch"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell RNA-seq analysis of murine and human mesenchymal stem/stromal cells reveals macrophage-like phenotypic plasticity","description":"This dataset contains single-cell RNA-seq profiles generated to investigate the phenotypic plasticity of mesenchymal stem/stromal cells (MSCs), with a focus on freshly isolated murine CD45-, TER119-, Sca-1+, PDGFRα+ (PαS) cells. Following transplantation into irradiated recipients, a subset of PαS cells acquired macrophage-like features, expressing CD45, CD68, and CSF1R/CD115. In vitro culture of PαS cells in macrophage differentiation media induced an M2-like signature (CD45, CD68, CD206) via CSF1R-dependent pathways. The dataset includes murine MSC samples from the C57/BL6 strain. The sequencing data support the identification of macrophage-like transcriptional clusters within the PαS population.","dates":{"release":"2026-01-23T00:00:00Z","modification":"2026-01-23T16:01:33.659Z","creation":"2026-01-08T21:34:36.386Z"},"accession":"E-MTAB-16511","cross_references":{"ENA":["ERP187402"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0004184"]}}