run_metadata: 61709

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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
61709	SRR12967073	SRX9419611	SRS7634948	SRP290840	PRJNA673886	Paternal hypoxia exposure primes offspring for increased hypoxia resistance	GSE160662	Other	Environmental challenges experienced by an organism can have multiple effects at an individual level with recent work also suggesting these challenges may affect their unexposed offspring. In a time of rapid environmental change understanding whether environmental challenges experienced by organisms could increase the fitness of future generations to survive these same stressors is critically needed. Low dissolved oxygen is a common environmental challenge that aquatic organisms encounter resulting in numerous physiological phenotypic and epigenetic changes. In this study we use zebrafish Danio rerio as a model to investigate how paternal hypoxia experience impacts subsequent progeny. Males were exposed to moderate hypoxia 11 13 kPA for xxx weeks bred to create an F1 generation and progeny underwent an acute hypoxia 0 1 kPA tolerance assay. Using time to loss of equilibrium and loss of equilibrium frequency as measured of hypoxia resistance we show that paternal exposure to hypoxia endow offspring with a greater tolerance to acute hypoxia compared to offspring of unexposed males though there are strong family x treatment effects. In addition to phenotypic alternations we also investigated changes in gene expression in offspring. We conducted RNA Seq on whole fry and detected 91 differentially expressed genes including two hemoglobin genes that are significantly upregulated by more than 4 fold in the offspring of hypoxia exposed males. Moreover the offspring which maintained equilibrium the longest showed the greatest upregulation in hemoglobin expression. Paternal exposures to physiological challenges are thus able to impact the phenotype and gene expression of their unexposed progeny. We conducted whole genome bisulfite sequencing WGBS on the sperm of parental males to assess whether changes in progeny phenotype and gene expression are underpinned by changes in DNA methylation. While we observed coupling of methylation levels in the parental sperm and gene expression in progeny overall we did not detect differential methylation at any of the differentially expressed genes suggesting that another epigenetic mechanism is responsible for the observed changes in gene expression. Overall our findings suggest that a 'memory' of past hypoxia exposure is maintained and that this environmentally induced information is transferred to subsequent generations pre acclimating progeny to cope with hypoxic conditions. Overall design: Zebrafish males were exposed to moderate hypoxia 11 13 kPA for xxx weeks and bred to create an F1 generation. To evaluate changes in gene expression we conducted RNA Seq on 20 dpf fry from control and hypoxia treated males. Additionally to evaluate changes in DNA methylation patterns we conducted whole genome bisulfite sequencing WGBS on the sperm of parental males.		pubmed:36038899		RNA seq fry no treatment 1	GSM4876599		source name:Fry\|treatment:No treatment\|tissue:whole organism\|generation:F1	RNA seq fry no treatment 1	Trimming using TrimGalore ! v0.6.4 quality threshold 20 hard trimming 10bp Reads were aligned against Danio rerio genome GCRz11 using using HISAT2 v2.2.0 and Bismark v0.22.3 for RNA seq and PBAT reads respectively For RNA seq analysis expression was summarized sample by sample at the gene level using featureCounts v2.0.0. For methylation analysis BAM files were deduplicated and CpG calls were extracted using bismark methylation extractor. Genome build: GCRz11 Supplementary files format and content: Processed files contain counts for gene expression analysis and individual CpG calls proccesed by Bismark for methylation analysis.	Fry	In November 2016 nine mpf male zebrafish AB wild type; n=20/treatment were exposed to hypoxic conditions 11 13 kPA oxygen; 53.1 60% air saturation or control conditions 21 kPA for two weeks.	Total RNA from 6 whole fry 3 control offspring 3 treatment offspring was extracted using a Zymo Duet extraction kit Zymo NZ. Total nucleic acids for methylation analysis were purified using the Bio On Magnetic Beads BOMB approach Oberacker et al. 2018. Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA sample preparation kit Illumina as per the manufacturer's instructions. Bisulfite coverted genomic libraries were prepared using a modified post bisulfite adapter tagging method.	Breeding and husbandry took place within the Otago Zebrafish Facility OZF a temperature controlled facility maintained at 25 27°C pH 7 7.8 and conductivity 300 500 µS. Fish were maintained in a Tecniplast re circulating system Tecniplast Varese Italy under a 14:10 light:dark photoperiodic cycle with 30 minutes of simulated dawn and dusk at the start and end of each day.	treatment:No treatment\|tissue:whole organism\|generation:F1	GSM4876599	GSM4876599: RNA seq fry no treatment 1; Danio rerio; RNA Seq	GSM4876599		1	Total RNA from 6 whole fry 3 control offspring 3 treatment offspring was extracted using a Zymo Duet extraction kit Zymo NZ. Total nucleic acids for methylation analysis were purified using the Bio On Magnetic Beads BOMB approach Oberacker et al. 2018. Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA sample preparation kit Illumina as per the manufacturer's instructions. Bisulfite coverted genomic libraries were prepared using a modified post bisulfite adapter tagging method.	GEO Accession:GSM4876599	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP290840			RNA_seq_fry_no_treatment_1.fastq.gz	fastq	1996165600.0	19961656.0	GSM4876599 r1	0:100	A:489777705;C:492746137;G:478910532;T:534723587;N:7639	100				489777705	492746137	478910532	534723587	7639	SRX9419611	SRS7634948	SRA1152608	GEO	Anatomy, University of Otago	1	0.95819		0.03758		0.70151		0.46991		100		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		New Zealand	2020-11-02	Undetermined	Adult	Whole Organism	All anatomical structures