{"database": "metadata", "table": "run_metadata", "rows": [[39946, "SRR2541818", "SRX1297640", "SRS1095796", "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.", null, "pubmed:29272799", null, "zfish 1ppm R1", "GSM1899549", null, "source name:ovary|tissue:ovary|strain:EK|mehg exposure:1 ppm", "zfish 1ppm R1", "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 \u201cTruSeq RNA Sample Preparation Guide\u201d 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:1 ppm", "GSM1899549", "GSM1899549: zfish 1ppm R1; Danio rerio; RNA Seq", "GSM1899549", null, "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 \u201cTruSeq RNA Sample Preparation Guide\u201d 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:GSM1899549", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP064360", null, null, "run448.R1-1ppm_CGATGT_L003_R1.fastq.gz run448.R1-1ppm_CGATGT_L003_R2.fastq.gz", "fastq fastq", 2389310540.0, 11828270.0, "GSM1899549 r1", "0:101 1:101", "A:636881481;C:557085654;G:551199582;T:638074409;N:6069414", 101, 101, null, null, 636881481, 557085654, 551199582, 638074409, 6069414, "SRX1297640", "SRS1095796", "SRA302185", "GEO", "School of Freshwater Sciences, University of Wisconsin-Milwaukee", 2, 0.92963, 0.92829, 0.02114, 0.02117, 0.74809, 0.74917, 0.45534, 0.45205, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-09-30", "Adult", "Adult", "Gonad", "Reproductive System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["39946"], "units": {}, "query_ms": 10.51300899416674}