{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Emily Brockmann"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17280"],"description":["COL2A1-associated skeletal dysplasias and growth disorders affect cartilage extracellular matrix and endochondral growth, but patient growth-plate tissue is largely inaccessible, limiting non-invasive modelling of disease- and growth-factor-responsive molecular programs. Here, we generated chondrogenically induced urine-derived stem/stromal cells (chUSCs) from two individuals with heterozygous pathogenic COL2A1 variants. Single-cell RNA sequencing was performed in two patient-derived lines under control and IGF1-treated conditions."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Single-cell gene expression libraries were generated using the 10x Genomics GEM-X 3' v4 OCM 4-plex workflow according to the manufacturer's instructions.","Sample Collection - Urine samples were obtained from three individuals with clinically classified pathogenic heterozygous COL2A1 variants and from three healthy control donors after written informed consent.","Nucleic Acid Extraction - For single-cell RNA-seq, chondrogenically induced cultures were dissociated using Accutase for 15 min. Cell number and viability were assessed using acridine orange/propidium iodide staining on a Revvity cell counter before library preparation.","Growth Protocol - Urine-derived stem/stromal cells (USCs) were isolated from freshly collected urine samples. Samples were processed as soon as possible by centrifugation at 300 × g for 5 min. Cell pellets were washed in phosphate-buffered saline containing 1% penicillin/streptomycin, centrifuged again, and resuspended in expansion medium. Cells were seeded on 0.2% gelatin-coated culture vessels and expanded in α-MEM Eagle medium supplemented with 20% fetal bovine serum, 5 ng/mL basic fibroblast growth factor, and 1% penicillin/streptomycin at 37°C and 5% CO2. Medium was changed three times per week. Cells were passaged with trypsin, expanded before or around passage 7, cryopreserved, and thawed for differentiation and sequencing.","Sample Treatment - For chondrogenic induction, USCs were cultured as two-dimensional monolayers on 0.2% gelatin using the StemPro Chondrogenesis Differentiation Kit supplemented with 1% penicillin/streptomycin. Medium was changed three times per week. Single-cell RNA-seq samples were harvested after 2 weeks of chondrogenic induction. For IGF1-treated single-cell RNA-seq samples, recombinant human IGF1 was added to the chondrogenic differentiation medium at 150 ng/mL for the full duration of differentiation. Matched control cultures received chondrogenic differentiation medium without IGF1.","Sequencing - Libraries were sequenced on an Illumina NovaSeq X Plus platform. Bulk RNA-seq libraries generated paired-end reads with a read length of 159 bp."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Single-cell RNA-seq FASTQ files were processed using Cell Ranger Multi version 10.0.0 with a GRCh38 reference genome."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RAN-seq of total RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Steffen Uebe","Emily Brockmann","Alexander Schulz","Christian Thiel"],"additional_accession":[]},"is_claimable":false,"name":"Single-Cell RNA Sequencing of chondrogenically induced urine-derived stem/stromal cells from patients with COL2A1 variants under control and IGF1-treated conditions","description":"COL2A1-associated skeletal dysplasias and growth disorders affect cartilage extracellular matrix and endochondral growth, but patient growth-plate tissue is largely inaccessible, limiting non-invasive modelling of disease- and growth-factor-responsive molecular programs. Here, we generated chondrogenically induced urine-derived stem/stromal cells (chUSCs) from two individuals with heterozygous pathogenic COL2A1 variants. Single-cell RNA sequencing was performed in two patient-derived lines under control and IGF1-treated conditions.","dates":{"release":"2026-09-30T00:00:00Z","modification":"2026-09-30T01:00:52.439Z","creation":"2026-07-02T14:45:54.964Z"},"accession":"E-MTAB-17280","cross_references":{"ENA":["ERP196098"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}