{"database": "metadata", "table": "run_metadata", "rows": [[39969, "SRR2567879", "SRX1309240", "SRS1102449", "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\u2014a 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 0.03\u00b5M 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 \u00b5M MeHg and exposure 0.03 \u00b5M MeHg groups.", "parent bioproject:PRJNA297897", null, null, "C6B", "GSM1902830", null, "source name:Brain|tissue:Brain|generation:F3|strain:EK|mehg conc:0\u00b5M MeHg", "C6B", "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 \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. Sequencing depth was 14 32 million reads per sample.", "Eggs of EK strain zebrafish were exposed to methylmercury\u00a00.0 and 0.03\u03bcM with ethanol as the vehicle for 24 hours  then raised normally.\u00a0This represents the F1 generation of each respective lineage. F2 and F3 generations were created for each lineage.\u00a0The F2 and F3 generations were never exposed to exogenous MeHg.\u00a0", "tissue:Brain|generation:F3|strain:EK|mehg conc:0\u00b5M MeHg", "GSM1902830", "GSM1902830: C6B; Danio rerio; RNA Seq", "GSM1902830", null, "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 \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. Sequencing depth was 14 32 million reads per sample.", "GEO Accession:GSM1902830", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP064535", null, null, "run483.C6B_AGTCAA_L001_R1.fastq.gz run483.C6B_AGTCAA_L001_R2.fastq.gz", "fastq fastq", 1621396228.0, 8026714.0, "GSM1902830 r1", "0:101 1:101", "A:445607490;C:367908457;G:364215334;T:442547659;N:1117288", 101, 101, null, null, 445607490, 367908457, 364215334, 442547659, 1117288, "SRX1309240", "SRS1102449", "SRA303285", "GEO", "Carvan Lab, School of Freshwater Sciences, University of Wisconsin-Milwaukee", 2, 0.93412, 0.93278, 0.10925, 0.10996, 0.69069, 0.69581, 0.52912, 0.5284, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-10-06", "Undetermined", "Embryo", "Brain", "Nervous 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": ["39969"], "units": {}, "query_ms": 10.572668004897423}