run_metadata: 30513

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
30513	SRR27764783	SRX23429746	SRS20284187	SRP486526	PRJNA1070616	Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response	GSE254466	Transcriptome Analysis	The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l also known as Scaf1 promotes CIII CIV super assembly and energetic efficiency in zebrafish mice and humans. Here we studied the role of a second member of the Cox7a family Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism. Already in homeostatic conditions cox7a1 / hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical revealing that there is a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 / mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq. 4 pools each comprising 5 ventricles were sequenced per condition.		pubmed:38701784		Cardiac ventricle cox7a1 / replicate 3	GSM8042778		source name:Cardiac Ventricle\|tissue:Cardiac Ventricle\|genotype:Cox7a mut\|treatment:7days post cryoinjury\|geo loc name:missing\|collection date:missing	Cardiac ventricle cox7a1 / replicate 3	Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts tab seprated values	Cardiac Ventricle		4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		tissue:Cardiac Ventricle\|genotype:Cox7a mut\|treatment:7days post cryoinjury	GSM8042778	GSM8042778: Cardiac ventricle cox7a1 / replicate 3; Danio rerio; RNA Seq	GSM8042778 r1	GSM8042778	1	4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000		SRP486526			KO_9_Directional_S7_R1_001.fastq.gz	fastq	6466746100.0	64667461.0	GSM8042778 r1	0:100	A:1708351950;C:1464168743;G:1452219209;T:1841033764;N:972434	100				1708351950	1464168743	1452219209	1841033764	972434	SRX23429746	SRS20284187	SRA1793874	University of Bern	University of Bern												B		usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown		Switzerland	2024-01-29	Undetermined	Adult	Heart	Cardiovascular System