run_metadata: 43811

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
43811	SRR6144818	SRX3256914	SRS2570595	SRP119524	PRJNA413523	Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny	GSE104692	Transcriptome Analysis	Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in ß oxidation observed in the progeny corresponded to the increase in peroxisomal ß oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition estrogen signalling was found to be affected by parental high dietary ARA levels where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced in total 24 fish was analyzed		pubmed:30070994;pubmed:31398226		high ARA f0 13	GSM2805931		source name:Liver\|treatment:High arachidonic acid group\|generation:F0 generation\|tissue:liver	high ARA f0 13	Sequence quality was assessed using FastQC v0.11.5 finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al. Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt	Liver	For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF	Livers were briefly rinsed in 1x PBS snap frozen with liquid nitrogen and stored at 80°C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop® ND 1000 Spectrophotometer NanoDrop Technologies USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit Agilent Technologies USA. RIN values from the 12 extracted RNA samples were on average 9.06 ± 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina	F0 embryos were collected randomly and larvae were fed with Gemma micro® Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 ± 1°C 14 h light 10 h dark period conductivity of 500 µS and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.	treatment:High arachidonic acid group\|generation:F0 generation\|tissue:liver	GSM2805931	GSM2805931: high ARA f0 13; Danio rerio; RNA Seq	GSM2805931		1	Livers were briefly rinsed in 1x PBS snap frozen with liquid nitrogen and stored at 80°C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop® ND 1000 Spectrophotometer NanoDrop Technologies USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit Agilent Technologies USA. RIN values from the 12 extracted RNA samples were on average 9.06 ± 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina	GEO Accession:GSM2805931	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP119524			high_ARA_f0_13.fastq	fastq	575303888.0	7569788.0	GSM2805931 r1	0:76 1:0	A:144137425;C:131780222;G:135118510;T:164264223;N:3508	76	0			144137425	131780222	135118510	164264223	3508	SRX3256914	SRS2570595	SRA617763	GEO	Feed Safety, National Institute of nutrition and seafood research (NIFES)	1	0.9563		0.06221		0.79482		0.56822		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		Norway	2017-10-06	Multi-stage	Multi-stage	Liver	Liver and Biliary System