{"database": "metadata", "table": "run_metadata", "rows": [[42543, "SRR5742105", "SRX2947052", "SRS2306348", "SRP110158", "PRJNA391470", "SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE NON IONIC SURFACTANT NONYLPHENOL NP.", "GSE100369", "Transcriptome Analysis", "We report the effects of exposure to the endocrine disruptor nonylphenol NP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and inflammation  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.", null, "pubmed:30563618", null, "CL60", "GSM2679632", null, "tissue:Liver|agent:Control|Sex:male", "CL60", "Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp\u2019s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content:   tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2", "Liver", "Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29\u00baC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 1000 nM of 17\u03b2 estradiol E2  one tank contained 100 nM of nonylphenol NP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70\u00baC for molecular biology analysis.", "Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.", null, "agent:Control|Sex:Male", "GSM2679632", "GSM2679632: CL60; Danio rerio; RNA Seq", "GSM2679632", null, "1", "Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.", "GEO Accession:GSM2679632", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP110158", null, null, "M-CL60.fa.fastq.gz", "fastq", 118617576.0, 2824228.0, "GSM2679632 r1", "0:42", "A:31502482;C:23344593;G:29696129;T:34068892;N:5480", 42, null, null, null, 31502482, 23344593, 29696129, 34068892, 5480, "SRX2947052", "SRS2306348", "SRA579535", "GEO", "Walton RS311, Pathology, Medical University of South Carolina", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-06-22", "Undetermined", "Undetermined", "Liver", "Liver and Biliary 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": ["42543"], "units": {}, "query_ms": 10.699948004912585}