{"database": "metadata", "table": "run_metadata", "rows": [[25346, "SRR25868019", "SRX21589434", "SRS18767007", "SRP457978", "PRJNA1011839", "fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk]", "GSE242134", "Transcriptome Analysis", "In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.", "parent bioproject:PRJNA1011837", "pubmed:38431640", null, "20m des trunk group 2", "GSM7749540", null, "source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing", "20m des trunk group 2", "Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts", "20 mpf trunk muscle", null, "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection", "WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28\u00b0C", "age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / ", "GSM7749540", "GSM7749540: 20m des trunk group 2; Danio rerio; RNA Seq", "GSM7749540 r1", "GSM7749540", "1", "Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457978", null, "loader:fastq load.py", "P25101_111_S22_L003_R1_001.fastq.gz P25101_111_S22_L003_R2_001.fastq.gz", "fastq fastq", 28432907098.0, 94148699.0, "GSM7749540 r1", "0:151 1:151", "A:7530352460;C:6691515017;G:7032193813;T:7178705133;N:140675", 151, 151, null, null, 7530352460, 6691515017, 7032193813, 7178705133, 140675, "SRX21589434", "SRS18767007", "SRA1703875", "Ume\u00e5 Univeristy", "Ume\u00e5 Univeristy", 2, 0.95304, 0.94619, 0.0303, 0.03073, 0.81288, 0.81734, 0.54159, 0.529, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Sweden", "2023-09-01", "Adult", "Adult", "Multi-tissue", "Multi-system"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["25346"], "units": {}, "query_ms": 11.007734996383078}