{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Sophie Franzmeier"],"organism":["Sus scrofa"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16179"],"description":["Satellite cells (SCs), the stem cell population of skeletal muscle, are crucial for growth and regeneration, and their dysfunction is increasingly recognized as a contributing factor to Duchenne muscular dystrophy (DMD). DMD is a severe, X-linked disorder caused by  DMD gene mutations, leading to loss of dystrophin expression in muscle tissue and a progressive muscle degeneration. Here, we provide RNA-seq data from wild-type (WT), dystrophin-deficient (DMD), and heterozygous (HET) pig SCs, representing a translational model for human DMD. Muscle biopsies were collected from fetal and 3-day-old animals, enzymatically digested, and subjected to magnetically activated cell sorting for SC purification. Purified cells were cultured under normal growth conditions in proliferation (PROL) and after induction to differentiate into multinucleated myotubes (DIFF), and total RNA was extracted for 3′ mRNA-seq. Libraries were prepared using NexteraXT and sequenced on a NextSeq550Dx. After quality control and deduplication, reads were aligned to the Sus scrofa reference genome, and gene counts were generated with STAR. Parts of this data have been previously published in a larger study and are now made fully accessible as an independent dataset. By capturing stage- and genotype-specific transcriptional signatures of SCs, this dataset offers new insights into the molecular defects associated with dystrophin-deficiency and serves as a reference resource for future studies investigating DMD pathogenesis."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - Purified SC were cultivated under standard conditions in Ham’s F10 Medium (GIBCO, Thermo Fisher) supplemented with 20% Fetal Bovine Serum (GIBCO), 1% Penicillin-Streptomycin (GIBCO), and 10 μg recombinant human basic fibroblast growth factor (PEPro Tech). Myoblast differentiation was induced by nutrient starvation using medium with 5% horse serum (Biozol).","Nucleic Acid Extraction - Total RNA from WT, DMD, and HET SCs was isolated using the NEB Monarch RNA Miniprep Kit in accordance with the manufacturer’s instructions. RNA concentration was determined with a Nanodrop 2000c spectrophotometer (Thermo Scientific) before proceeding with subsequent experiments. Cells were harvested at p6 and p7 after cultivation in normal growth medium to recapture the proliferation stage (PROL), and after 10 days in medium with reduced serum amount for the differentiation stage (DIFF).","Sample Collection - A detailed protocol for the isolation of myogenic satellite cells (SCs) for sample collection is provided in Franzmeier et al., 2025. In summary, tissue biopsies from intercostalis and pectoralis muscles were collected from WT, DMD, and HET animals immediately after euthanasia, and were minced manually with a scalpel blade. After enzymatic digestion with protease (Streptomyces griseus, Sigma Aldrich, 3.5 U/mg) and collagenase (Clostridium histolyticum, Sigma Aldrich, 800 U/mg), cell suspensions were subjected to magnetically activated cell sorting (MACS) using an indirect labelling approach and two sequential separation steps. Unwanted endothelial and hematopoietic cells were depleted by adding rabbit anti-CD31 (1:200, ab28364, Abcam) and rabbit anti-CD45 (1:200, ab10558, Abcam) antibodies together with magnetically conjugated anti-rabbit IgG(-) secondary antibodies (1:15, Miltenyi Biotec) to the cell suspension. Labelled cells were retained within a magnetic column placed on the MACS separator, and the flow-through was used for the subsequent separation step. SCs were targeted with mouse anti-Integrin-1 (1:200, abcam30388, Abcam), mouse anti-NCAM1 (1:200, ab9018, Abcam), and mouse anti-M-cadherin (1:200, sc-374093, Santa Cruz) and magnetically conjugated secondary anti-mouse IgG(-) antibodies (1:15, Miltenyi Biotec); again labelled cells were retained in the column allowing enrichment of the desired SC population.","Library Construction - Gene expression was quantified using an adapted 3’m RNA-seq protocol. 25 ng of total RNA was used for each sample and analysed as a technical duplicate. For library construction, polyA+ RNAs were selected with a unique molecular identifier (UMI) and a well-barcode for early pooling directly after cDNA synthesis. By RT-PCR using a template switch oligo with an integrated Illumina adapter sequence, second-strand synthesis was performed. Subsequently, purification and exonuclease◦I treatment were executed, followed by library pool amplification using NexteraXT DNA library prep Kit (Illumina). DNA was tagmented with Nextera transposons, and for library amplification, a 3’ enrichment PCR was performed during which i7 and i5 adapters were attached. After purification, the quantity of the library pool was measured with a Qubit Fluormeter 4.0 (Thermo Fisher Scientific) as well as average fragment size with a Labchip GX Touch 24 (Perkin Elmer/Revvity). Please see also Franzmeier et al., 2025.","Sequencing - The nucleic acid library was sequenced on a NextSeq550Dx (Illumina) using a 75-cycle high-output kit (Read 1:16◦cycle − UMI + barcode; Read 2: 76◦cycles − Insert).  Demultiplexing of RNAseq reads was performed using bcl2fastq (Illumina). R (version 4.1.2) command line tools fastQC and multiQC were used for quality control, and umi-tool dedup for deduplication. Reads were aligned to the Sus scrofa reference genome susScr3 using STAR aligner (version 2.7.10b), and gene counts were obtained with STAR (quantMode GeneCounts.) Please see also Franzmeier et al., 2025."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw data processing and normalization were performed in R (version 4.1.2) using the edgeR package."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 550","Nanodrop 2000c spectrophotometer"],"pubmed_abstract":["Recent studies on myogenic satellite cells (SCs) in Duchenne muscular dystrophy (DMD) documented altered division capacities and impaired regeneration potential of SCs in DMD patients and animal models. It remains unknown, however, if SC-intrinsic effects trigger these deficiencies at pre-contractile stages of myogenesis rather than resulting from the pathologic environment. In this study, we isolated SCs from a porcine DMD model and age-matched wild-type (WT) piglets for comprehensive analysis. Using immunofluorescence, differentiation assays, traction force microscopy (TFM), RNA-seq, and label-free proteomic measurements, SCs behavior was characterized, and molecular changes were investigated. TFM revealed significantly higher average traction forces in DMD than WT SCs (90.4 ± 10.5 Pa vs. 66.9 ± 8.9 Pa; <i>p</i> = 0.0018). We identified 1390 differentially expressed genes and 1261 proteins with altered abundance in DMD vs. WT SCs. Dysregulated pathways uncovered by gene ontology (GO) enrichment analysis included sarcomere organization, focal adhesion, and response to hypoxia. Multi-omics factor analysis (MOFA) integrating transcriptomic and proteomic data, identified five factors accounting for the observed variance with an overall higher contribution of the transcriptomic data. Our findings suggest that SC impairments result from their inherent genetic abnormality rather than from environmental influences. The observed biological changes are intrinsic and not reactive to the pathological surrounding of DMD muscle."],"study_type":["RNA-seq of coding RNA"],"species":["Sus scrofa"],"pubmed_title":["Transcriptome of Myogenic Stem Cells from a Porcine Duchenne Muscular Dystrophy Model.","Multi-Modal Analysis of Satellite Cells Reveals Early Impairments at Pre-Contractile Stages of Myogenesis in Duchenne Muscular Dystrophy."],"pubmed_authors":["Franzmeier S, Chakraborty S, Mortazavi A, Stöckl JB, Jian J, Pfarr N, Sabass B, Fröhlich T, Kaufhold C, Stirm M, Wolf E, Schlegel J, Matiasek K.","Franzmeier S, Chakraborty S, Mayr E, Pfarr N, Wolf E, Schlegel J, Stemmer K, Matiasek K.","Sophie Franzmeier"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq from myogenic satellite cells from a translational porcine model for Duchenne muscular dystrophy, heterozygous female carriers, and their healthy wild-type counterpart","description":"Satellite cells (SCs), the stem cell population of skeletal muscle, are crucial for growth and regeneration, and their dysfunction is increasingly recognized as a contributing factor to Duchenne muscular dystrophy (DMD). DMD is a severe, X-linked disorder caused by  DMD gene mutations, leading to loss of dystrophin expression in muscle tissue and a progressive muscle degeneration. Here, we provide RNA-seq data from wild-type (WT), dystrophin-deficient (DMD), and heterozygous (HET) pig SCs, representing a translational model for human DMD. Muscle biopsies were collected from fetal and 3-day-old animals, enzymatically digested, and subjected to magnetically activated cell sorting for SC purification. Purified cells were cultured under normal growth conditions in proliferation (PROL) and after induction to differentiate into multinucleated myotubes (DIFF), and total RNA was extracted for 3′ mRNA-seq. Libraries were prepared using NexteraXT and sequenced on a NextSeq550Dx. After quality control and deduplication, reads were aligned to the Sus scrofa reference genome, and gene counts were generated with STAR. Parts of this data have been previously published in a larger study and are now made fully accessible as an independent dataset. By capturing stage- and genotype-specific transcriptional signatures of SCs, this dataset offers new insights into the molecular defects associated with dystrophin-deficiency and serves as a reference resource for future studies investigating DMD pathogenesis.","dates":{"release":"2025-12-11T00:00:00Z","modification":"2025-12-11T02:01:56.53Z","creation":"2025-11-20T19:04:00.189Z"},"accession":"E-MTAB-16179","cross_references":{"pubmed":["40558519"],"ENA":["ERP185435"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"],"doi":["10.3390/cells14120892"]}}