biostudies-arrayexpressEmily BrockmannHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17279COL2A1-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 three individuals with heterozygous pathogenic COL2A1 variants and three healthy controls. Bulk RNA sequencing compared patient-derived and control chUSCs.biostudies-arrayexpressSample 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.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.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.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. Bulk RNA-seq samples were harvested after 3 weeks of chondrogenic induction.Nucleic Acid Extraction - Total RNA was extracted from chondrogenically induced urine-derived stem/stromal cell cultures using the laboratory's standard column-based RNA-seq workflow with genomic DNA removal. RNA quality was assessed before library preparation, and all included samples passed the laboratory quality threshold.Library Construction - Stranded mRNA sequencing libraries were prepared from total RNA using the Illumina stranded mRNA library preparation workflow according to the manufacturer's instructions.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Raw sequencing output was demultiplexed using Illumina DRAGEN. Reads corresponding to unwanted RNA species were filtered using bwa mem version 0.7.17 and samtools. Filtered reads were converted back to FASTQ using GATK SamToFastq and aligned to the human hg38 reference genome with Ensembl gene annotations using STAR version 2.7.10a.Data Transformation - Gene-level counts were generated using featureCounts version 2.0.1.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XRNA-seq of total RNAHomo sapiensSteffen UebeEmily BrockmannAlexander SchulzChristian ThielfalseRNA-Seq of patient-derived COL2A1-mutant chondrogenic urine-derived stem cells against unaffected controlsCOL2A1-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 three individuals with heterozygous pathogenic COL2A1 variants and three healthy controls. Bulk RNA sequencing compared patient-derived and control chUSCs.2026-09-30T00:00:00Z2026-09-30T01:00:43.351Z2026-06-25T13:45:24.68ZE-MTAB-17279ERP195724EFO_0002944EFO_0004170EFO_0009653EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969