{"database": "metadata", "table": "run_metadata", "rows": [[37109, "SRR924081", "SRX316720", "SRS454027", "SRP026400", "PRJNA210007", "Genome wide identification of molecular pathways and biomarkers in response to arsenic exposure in zebrafish liver", "GSE48427", "Transcriptome Analysis", "In the present study  we employed the RNA sequencing platform to examine the molecular response of zebrafish liver to arsenic exposure and carry out detailed transcriptomic analyses for further understanding of molecular toxicity. We found that several important biological processes were perturbed by arsenic exposure  including oxidation reduction  translation  iron ion transport  cell redox and homeostasis  as well as related pathways in metabolism and diseases. Furthermore  as there are currently no biomarker genes available for predicting arsenic exposure  we took the advantage of RNA sequencing platform to identify most suitable biomarker genes from top responsive genes to arsenic exposure. We first validated these top responsive genes by RT qPCR in zebrafish and then in Japanese medaka Oryzias latipes at individual fish level for more robustly responsive genes across different fish species. Overall design: Transcriptome profiling of arsenic treated sample and control sample were generated by deep sequencing using three prime RNA SAGE on the SOLiD system.", null, "pubmed:24176670;pubmed:23922661", null, "Arsenic treated zebrafish liver", "GSM1177836", null, "source name:liver  arsenic|genotype/variation:wildtype|tissue:liver|age:3 month|treatment:arsenate sodium", "Arsenic treated zebrafish liver", "The SOLiD generated RNA Seq reads were 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maximum mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 58 Supplementary files format and content: Tab delimited text file. The mapped transcripts are listed with GI  RefSeq accession  and expression levels in TPM.", "liver  arsenic", "3 mpf wildtype zebrafish were treated for 96 hrs. Sodium arsenate treatment was conducted in 3 L tanks with around 15 adults and water was changed every day.", "Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype/variation:wildtype|tissue:liver|age:3 month|treatment:arsenate sodium", "GSM1177836", "GSM1177836: Arsenic treated zebrafish liver; Danio rerio; RNA Seq", "GSM1177836", null, "1", "Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", "GEO Accession:GSM1177836", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP026400", null, null, "solid0518_20101014_Gong_1_SetA_F3_QV_2_2Arsenic.qual solid0518_20101014_Gong_1_SetA_F3_2_2Arsenic.csfasta", "SOLiD_native SOLiD_native", 477279215.0, 13636549.0, "GSM1177836 r1", "0:35", "0:135280436;1:121477647;2:102046207;3:117826846;.:648079", 35, null, null, null, null, null, null, null, null, "SRX316720", "SRS454027", "SRA091803", "GEO", "National University of Singapore", 1, 0.0161, null, 0.00302, null, 0.99334, null, 0.51629, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2013-06-28", "Adult", "Adult", "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": ["37109"], "units": {}, "query_ms": 8.811622999928659}