run_metadata: 39947

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
39947	SRR2541817	SRX1297639	SRS1095797	SRP064360	PRJNA297460	Female Reproductive Impacts of Dietary Methylmercury in Yellow Perch Perca flavescens and Zebrafish Danio rerio	GSE73615	Transcriptome Analysis	This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch Perca flavescens and zebrafish Danio rerio reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle mimicking a realistic exposure scenario and in adult yellow perch for twenty weeks capturing early seasonal ovarian development. In zebrafish several genes involved in reproductive processes were shown to be dysregulated by RNA seq and QPCR but no significant phenotypic or physiological changes were observed with ovarian staging fecundity or embryo mortality. Yellow perch did not appear to be affected by MeHg either at a molecular level as assessed by QPCR of eight genes in the pituitary liver and ovary tissue or a physiological level as seen with ovarian somatic index circulating estradiol and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish. Overall design: 12 samples of total RNA isolated from adult zebrafish ovaries were analyzed. Each exposure group 1 3 and 10 ppm MeHg had three replicates as did the vehicle control. Each sample was comprised of pooled total RNA of up to 6 individual fish.		pubmed:29272799		zfish 0ppm R3	GSM1899548		source name:ovary\|tissue:ovary\|strain:EK\|mehg exposure:0 ppm	zfish 0ppm R3	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 The cleaned reads for each sample were independently aligned to the reference zebrafish genome Zv9 UCSC using TopHat The alignment output from TopHat was converted into a transcriptome using Cufflinks v. 2.2.1 and alignment data was confirmed using RNAseQC against the Zv9 reference transcriptome of zebrafish Sample specific transcriptomes were assembled using Cufflinks with the Zv9 transcriptome as a reference to correct fragment biases by better identifying the start/end point of each exon Transcriptomes from each sample were merged into an ovary specific transcriptome using Cuffmerge Differential expression was conducted with Cuffdiff using pooled dispersion geometric normalization and the merged ovary transcriptome. Genome build: UCSC Zv9 Supplementary files format and content: Cuffdiff outputs FPKM files which show expression values. Included in ovary.zip	ovary	Ovaries were flash frozen in RNA later and placed on dry ice immediately post dissection until proper storage at 80C.	High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. 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.	Adult EK female zebrafish were exposed to MeHg 0 1 3 or 10 ppm with ethanol as the vehicle for an entire life cycle starting with maternal exposure. Fish were exposed until euthanized.	tissue:ovary\|strain:EK\|mehg exposure:0 ppm	GSM1899548	GSM1899548: zfish 0ppm R3; Danio rerio; RNA Seq	GSM1899548		1	High quality total RNA was extracted from the ovary using Direct zol* RNA MiniPrep kit Zymo Research. Total RNA for each sample was comprised of pooled RNA from up to six individual fish in order to reduce biological variance. 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.	GEO Accession:GSM1899548	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP064360			run448.R3-control_GGCTAC_L003_R1.fastq.gz run448.R3-control_GGCTAC_L003_R2.fastq.gz	fastq fastq	1772836840.0	8776420.0	GSM1899548 r1	0:101 1:101	A:479859924;C:405519938;G:400658916;T:482250457;N:4547605	101	101			479859924	405519938	400658916	482250457	4547605	SRX1297639	SRS1095797	SRA302185	GEO	School of Freshwater Sciences, University of Wisconsin-Milwaukee	2	0.91754	0.91556	0.02431	0.02395	0.74998	0.75012	0.45157	0.45334	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		United States	2015-09-30	Adult	Adult	Gonad	Reproductive System