{"database":"ENA","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Fastqsanger.gz":["ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR855/007/SRR8559097/SRR8559097.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR855/006/SRR8559096/SRR8559096.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR855/009/SRR8559099/SRR8559099.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR855/000/SRR8559100/SRR8559100.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR855/005/SRR8559095/SRR8559095.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR855/004/SRR8559094/SRR8559094.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR855/008/SRR8559098/SRR8559098.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR855/003/SRR8559093/SRR8559093.fastq.gz"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Genomics"],"center_name":["Pediatric Neuromuscular Laboratory, The Institute of Neurology, Schneider Children's Medical Center of Israel"],"full_dataset_link":["https://www.ebi.ac.uk/ena/browser/view/PRJNA521797"],"scientific_name":["Mus musculus"],"tag":["xref:PubMed:31348492"],"long_description":["Congenital muscular dystrophy type-1A (Lama2-CMD) and Duchenne Muscular dystrophy (DMD) result from deficiencies of laminin-α2 and dystrophin proteins, respectively. Although both proteins strengthen the sarcolemma, they are implicated in clinically distinct phenotypes. We used RNA-deep sequencing (RNA-Seq) of dy2J/dy2J, Lama2-CMD mouse model, skeletal muscle at 8 weeks of age to elucidate disease pathophysiology. This study is the first report of dy2J/dy2J model whole transcriptome profile. RNA-Seq of the mdx mouse model of DMD and WT mouse was carried as well in order to enable a novel comparison of dy2J/dy2J to mdx. A large group of shared differentially expressed genes (DEG) were found in dy2J/dy2J and mdx models (1,834 common DEG, (FDR) < 0.05). Enrichment pathway analysis using Ingenuity Pathway Analysis (IPA) showed enrichment of inflammation, fibrosis, cellular movement, migration and proliferation of cells, apoptosis and necrosis in both mouse models (p-values 3E-10 – 9E-37). Via Canonical pathway analysis Actin cytoskeleton, Integrin, ILK, NF-kB, Renin-angiotensin, calcium signaling were also enriched and upregulated in both models (FDR<0.05). Interestingly, significant downregulation of Pax7 was detected in dy2J/dy2J compared to upregulation of this key regeneration gene in mdx mice. Pax3 and Mamstr genes were also downregulated in dy2J/dy2J compared to WT mice. These results may explain the distinct disease course and severity in these models. While the mdx model at that stage shows massive regeneration, the dy2J/dy2J shows progressive dystrophic process. Our data deepen our understanding of the molecular pathophysiology and suggest new targets for additional therapies to upregulate regeneration in Lama2-CMD. Overall design: Quadriceps muscle biopsies from male Wild-type (n=14), dy2J/dy2J (n=11) and mdx (n=15) mice were recruiting at the age of 8 weeks to the experiment in order to analyzed differences in the transcriptome content. Biopsies were taken from each mouse for RNA isolation and subjected for RNA-Seq evaluation. The RNA from WT or mdx genotype was pooled into three batches, 4-6 RNA samples in each pool. Samples from dy2J mice were divided into two batches, 5-6 samples per pool."],"repository":["ENA"],"name_synonyms":["Ribonucleic, muscle system, determination, Laboratory, Mus domesticus, musculature system, DXS206, muscular dystrophy, A4, muscles, Muskelsystem, DXS164, House Mouse, TYPE, DAGA4, House, Gene Products, Mus musculus domesticus, Whole Transcriptome Shotgun Sequencing, merosin, MAM, Mice, SCG3, Non Polyadenylated, RNA Gene Products, congenital MD, camptomelic dysplasia, Muscle Tissues, Swiss, Tissues, Tissue, Swiss Mice, DXSmh7, DXSmh9, BMD, Non-Polyadenylated RNA, muscule system, Cmpd1/Sra1, Duchenne type, DXS239, house mouse, acampomelic campomelic dysplasia with autosomal Sex reversal, Cmd1, DXS230, dys, RNA, ribose nucleic acid, musculi, set of muscles, ribonucleic acids, mouse, set of skeletal muscles, RNA-seq, dy, RNS, Muscle, mice C57BL/6xCBA/CaJ hybrid, Mus muscaris, LGMD2C, Dp71, Mus, yeast nucleic acid, Ribonukleinsaeure, chemical analysis, pentosenucleic acids, Ribonucleic acids, 5830440B04, Dp427, mKIAA4087, mdx, ribonucleic acid, Acid, Mus musculus, muscles set, muscle group., CMPD1, DMDA1, pke, Severe dystrophinopathy, mice, Non Polyadenylated RNA, motor system, Swiss Mouse, Non-Polyadenylated, House Mice, Ribonucleic Acid, DXS142, pseudohypertrophic progressive, DMD, mer, CMD3B, DXS268, Cmpd, DXS269, domesticus, Laboratory Mice, DXS270, DXS272, DMDA, SCARMD2, musculature, MRX85, Mouse, assay, LAMM, Muscle Tissue, campomelic dysplasia with autosomal Sex reversal, Laboratory Mouse"],"description_synonyms":["Ribonucleic, muscle system, determination, Laboratory, Mus domesticus, musculature system, DXS206, muscular dystrophy, A4, muscles, Muskelsystem, DXS164, House Mouse, TYPE, DAGA4, House, Gene Products, Mus musculus domesticus, Whole Transcriptome Shotgun Sequencing, merosin, MAM, Mice, SCG3, Non Polyadenylated, RNA Gene Products, congenital MD, camptomelic dysplasia, Muscle Tissues, Swiss, Tissues, Tissue, Swiss Mice, DXSmh7, DXSmh9, BMD, Non-Polyadenylated RNA, muscule system, Cmpd1/Sra1, Duchenne type, DXS239, house mouse, acampomelic campomelic dysplasia with autosomal Sex reversal, Cmd1, DXS230, dys, RNA, ribose nucleic acid, musculi, set of muscles, ribonucleic acids, mouse, set of skeletal muscles, RNA-seq, dy, RNS, Muscle, mice C57BL/6xCBA/CaJ hybrid, Mus muscaris, LGMD2C, Dp71, Mus, yeast nucleic acid, Ribonukleinsaeure, chemical analysis, pentosenucleic acids, Ribonucleic acids, 5830440B04, Dp427, mKIAA4087, mdx, ribonucleic acid, Acid, Mus musculus, muscles set, muscle group., CMPD1, DMDA1, pke, Severe dystrophinopathy, mice, Non Polyadenylated RNA, motor system, Swiss Mouse, Non-Polyadenylated, House Mice, Ribonucleic Acid, DXS142, pseudohypertrophic progressive, DMD, mer, CMD3B, DXS268, Cmpd, DXS269, domesticus, Laboratory Mice, DXS270, DXS272, DMDA, SCARMD2, musculature, MRX85, Mouse, assay, LAMM, Muscle Tissue, campomelic dysplasia with autosomal Sex reversal, Laboratory Mouse"],"additional_accession":[]},"is_claimable":false,"name":"RNA-deep sequencing (RNA-Seq) analysis of dy2J/dy2J (Lama2-CMD mouse model), mdx (DMD mouse model) and Wild-type skeletal muscles","description":"RNA-deep sequencing (RNA-Seq) analysis of dy2J/dy2J (Lama2-CMD mouse model), mdx (DMD mouse model) and Wild-type skeletal muscles","dates":{"last_updated":"2025-09-24","first_public":"2020-04-17"},"accession":"PRJNA521797","cross_references":{"GEO":["GSE126416"],"taxon":["10090"],"PubMed":["31348492"]}}