run_metadata: 52957

This data as json

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52957	SRR9610846	SRX6374055	SRS5034864	SRP212268	PRJNA551601	Respiratory supercomplexes provide metabolic efficiency in zebrafish	GSE133487	Transcriptome Analysis	The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet were dissected and stored at 80°C.		pubmed:32496654		S0WT S 7 RNA Seq	GSM3910336		source name:WT Standard Diet Muscle\|Sex:female\|genotype/variation:WT\|treatment:Standard Diet\|tissue:Muscle	S0WT S 7 RNA Seq	Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto using Danio rerio cDNA. Next we used standard values for single end reads with 100 bootstraps fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11 release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the length eff length est counts and tpm of the “counts”. To be imported using tximport or sleuth.	WT Standard Diet Muscle	Zebrafish were fed during 6 weeks in two different diets: standard diet S gemma 300 3 times/day double diet DD gemma 300 5 times/day	Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System	Zebrafish were grown at same density 13 fish in 2 l tanks	Sex:female\|genotype/variation:WT\|treatment:Standard Diet\|tissue:Muscle	GSM3910336	GSM3910336: S0WT S 7 RNA Seq; Danio rerio; RNA Seq	GSM3910336		1	Adult zebrafish skeletal muscle were dissected and stored at 80°C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System	GEO Accession:GSM3910336	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP212268			S0WT_S_7__RNA_Seq_Directional_S48_L005_R1_001.fastq.gz	fastq	901161585.0	17669835.0	GSM3910336 r1	0:51	A:236551279;C:210199570;G:206723666;T:247589765;N:97305	51				236551279	210199570	206723666	247589765	97305	SRX6374055	SRS5034864	SRA914604	GEO	University of Bern	1	0.93688		0.05977		0.80119		0.50443		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		Switzerland	2019-06-28	Multi-stage	Multi-stage	Muscle	Muscular System