run_metadata: 9832

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
9832	ERR4029235	ERX4030551	ERS4513989	ERP121186	PRJEB37848	RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss	E-MTAB-8959	Transcriptome Analysis	The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss. Tissue types included liver skin muscle heart gut gill eye brain for all three species with additionally pyloric caeca kidney head kidney and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts FPKM or TPM were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation.	ENA FIRST PUBLIC:2020 04 30\|ENA LAST UPDATE:2020 04 16		Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.	ZF M 2	SAMEA6786309	CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences	ENA FIRST PUBLIC:2020 04 30T04:03:51Z\|ENA LAST UPDATE:2020 04 16T14:24:16Z\|External Id:SAMEA6786309\|INSDC center name:CIGENE Faculty of Biosciences The Norwegian University of Life Sciences\|INSDC first public:2020 04 30T04:03:51Z\|INSDC last update:2020 04 16T14:24:16Z\|INSDC status:public\|Submitter Id:E MTAB 8959:ZF M 2\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|organism part:muscle\|sample name:E MTAB 8959:ZF M 2\|scientific name:Danio rerio\|sex:male									Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss	E MTAB 8959:ZF M 2 p	ZF M 2 p	RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss	Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific.	Experimental Factor: organism part:muscle\|Experimental Factor: organism:Danio rerio	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500		ERP121186	Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss	ENA FIRST PUBLIC:2020 04 30\|ENA LAST UPDATE:2020 04 16	ZF-M-2_ATTACTCG-TAATCTTA_R2_001.fastq.gz ZF-M-2_ATTACTCG-TAATCTTA_R1_001.fastq.gz	fastq fastq	4318736184.0	17137842.0	E MTAB 8959:ZF M 2 ATTACTCG TAATCTTA R	0:126 1:126	A:1127118469;C:1038158146;G:1022013812;T:1130979521;N:466236	126	126			1127118469	1038158146	1022013812	1130979521	466236	ERX4030551	ERS4513989	ERA2508028	CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences\|European Nucleotide Archive	CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences\|European Nucleotide Archive	2	0.97246	0.97334	0.03723	0.03642	0.8061	0.8058	0.55712	0.55957	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown		Norway	2020-04-16	Adult	Adult	Multi-tissue	Multi-system