run_metadata: 39971

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
39971	SRR2567877	SRX1309238	SRS1102451	SRP064535	PRJNA297905	Methylmercury MeHg induced Transgenerational Inheritance of Brain Transcriptome in Zebrafish Danio rerio [brain]	GSE73794	Transcriptome Analysis	Methylmercury MeHg is a ubiquitous environmental toxicant that is often detected in the tissues of fish eating species. It has been well established that prenatal exposure to MeHg can lead to widespread brain damage and impaired neurological development resulting in defects ranging from severe cerebral palsy and cognitive deficits to impaired motor and sensory function. A wide range of environmental toxicants have been shown to induce transgenerational inheritance of diseases via changes in DNA methylation—a well known epigenetic modification. Our previous research has demonstrated that developmental MeHg exposure may yield transgenerational inheritance of neurological dysfunction in adult F3 lineage zebrafish via quantitative neurobehavioral assays that evaluated the visual startle response retinal electrophysiology and locomotor function. The objective of the current study was to examine the correlation between neurobehavioral phenotypes and the transcriptome activity in the brain and retina of F3 zebrafish by RNA sequencing RNAseq. Transcriptomic analyses of F3 generation MeHg treated zebrafish compared to control revealed significant gene dysregulation in both the brain and retina. There were 1648 and 138 differentially expressed genes in the retina and brain respectively FDR <0.05. Thirty five genes were commonly dysregulated in both organs. Gene set enrichment analysis revealed significantly enriched pathways including: neurodevelopment visual functions phototransduction and motor movement. Moreover commonly dysregulated genes were associated with circadian rhythm and metabolic pathways as well as arginine and proline metabolism. To our knowledge this is the first evidence of a transgenerational transcriptome induced by ancestral developmental exposure to MeHg in any species. If the transgenerational phenotypes transcriptome homologous biomarkers or similar molecular pathways hold true for human populations our findings have significant impact on global public health in terms of identifying the susceptible populations using biomarkers and preventing transgenerational inheritance of MeHg induced neurobehavioral deficits. Overall design: Eggs of EK strain zebrafish were exposed to methylmercury 0.0 and 0.03µM with ethanol as the vehicle for 24 hours then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg. The brain were collected from F3 generation fish of each lineage. 12 samples of total RNA isolated from adult zebrafish brain were analyzed. There were 6 biological replicates for vehicle control 0 µM MeHg and exposure 0.03 µM MeHg groups.	parent bioproject:PRJNA297897			C4B	GSM1902828		source name:Brain\|tissue:Brain\|generation:F3\|strain:EK\|mehg conc:0µM MeHg	C4B	Basecalling was performed using CASAVA 1.8.2. Adapters and low quality bases were removed from the initial 2x101bp Illumina TruSeq reads and trimmed using Cutadapt FastQC was used to ensure that cleaned reads were of higher quality than initial raw reads supplied by the sequencer The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat Aligned reads were used to generate count and fpkm data using Cuffnorm against Zv9 trainscriptome Genome build: UCSC Zv9 Supplementary files format and content: Tab delimited matrix of gene counts and FPKM normalized counts	Brain	The F1 generation embryos were exposed to MeHg. Brain of F3 generation was used for isolating RNA.	High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.	Eggs of EK strain zebrafish were exposed to methylmercury 0.0 and 0.03μM with ethanol as the vehicle for 24 hours then raised normally. This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage. The F2 and F3 generations were never exposed to exogenous MeHg.	tissue:Brain\|generation:F3\|strain:EK\|mehg conc:0µM MeHg	GSM1902828	GSM1902828: C4B; Danio rerio; RNA Seq	GSM1902828		1	High quality total RNA was extracted from the brain using RNeasy Micro Kit QIAGEN Valencia CA USA. Illumina TruSeq RNA Library Preparation and Sequencing was performed at the Biotechnology Center at the University of Wisconsin Madison. Each library was generated using a paired end approach following the Illumina “TruSeq RNA Sample Preparation Guide” and the Illumina TruSeq RNA Sample Preparation Kit Illumina Inc. San Diego CA USA. Samples were run with 12 samples per lane with 100 base pair paired end reads. Sequencing depth was 14 32 million reads per sample.	GEO Accession:GSM1902828	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP064535			run483.C4B_GGCTAC_L001_R2.fastq.gz run483.C4B_GGCTAC_L001_R1.fastq.gz	fastq fastq	787342874.0	3897737.0	GSM1902828 r1	0:101 1:101	A:221071638;C:173927956;G:172321230;T:219487360;N:534690	101	101			221071638	173927956	172321230	219487360	534690	SRX1309238	SRS1102451	SRA303285	GEO	Carvan Lab, School of Freshwater Sciences, University of Wisconsin-Milwaukee	2	0.93526	0.93535	0.10425	0.10623	0.69867	0.70307	0.53432	0.5404	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		United States	2015-10-06	Undetermined	Embryo	Brain	Nervous System