run_metadata: 25345

This data as json

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
25345	SRR25868018	SRX21589435	SRS18767008	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		20m des trunk group 3	GSM7749541		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 3	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		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°C	age:20 mpf\|tissue:trunk muscle\|strain:AB\|cell type:Trunk muscle myofibers\|genotype:desma / ;desmb /	GSM7749541	GSM7749541: 20m des trunk group 3; Danio rerio; RNA Seq	GSM7749541 r1	GSM7749541	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP457978		loader:fastq load.py	P25101_112_S23_L003_R1_001.fastq.gz P25101_112_S23_L003_R2_001.fastq.gz	fastq fastq	22210763348.0	73545574.0	GSM7749541 r1	0:151 1:151	A:5912051069;C:5198859790;G:5393563455;T:5706179211;N:109823	151	151			5912051069	5198859790	5393563455	5706179211	109823	SRX21589435	SRS18767008	SRA1703875	Umeå Univeristy	Umeå Univeristy	2	0.95876	0.95266	0.03675	0.03686	0.80085	0.80379	0.54105	0.54121	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk		Sweden	2023-09-01	Adult	Adult	Multi-tissue	Multi-system