{"database": "metadata", "table": "run_metadata", "rows": [[40353, "SRR3098581", "SRX1528548", "SRS1246176", "SRP068364", "PRJNA308582", "Transcriptional profiling through RNA seq of zebrafish larval liver post exposure to biliatresone  a biliary toxin.", "GSE76780", "Transcriptome Analysis", "We sequenced liver mRNA isolated from biliatresone treated zebrafish larvae and DMSO treated controls in order to elucidate the molecular pathways induced by biliatresone  a biliary toxin that is responsible for outbreaks of biliary atresia in Australian liverstock. Overall design: Liver mRNA profiles of biliatresone treated zebrafish larvae and DMSO treated controls were generated by deep sequencing  in duplicates.", null, "pubmed:27102575", null, "Biliatres1 1", "GSM2037740", null, "source name:liver|tissue:liver|treatment:Biliatres1", "Biliatres1 1", "Hiseq control software HCS was used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to zv9 whole genome using STAR. Python Htseq script was used to count the number of reads. Genome build: zv9 Supplementary files format and content: tab delimited text files include htseq count output.", "liver", "Zebrafish larvae were treated with biliatresone 0.5 ug/ml for four hours.", "Livers were dissected directly in to the lysis buffer RLT and RNA was harvested using the standard Qiagen protocol RNeasy Mini Kit. 1 ug of total RNA was used for sequecning library construction and the libraries were prepared using the Truseq Stranded Ribo Zero Library Prep Kit.", null, "tissue:liver|treatment:Biliatres1", "GSM2037740", "GSM2037740: Biliatres1 1; Danio rerio; RNA Seq", "GSM2037740", null, "1", "Livers were dissected directly in to the lysis buffer RLT and RNA was harvested using the standard Qiagen protocol RNeasy Mini Kit. 1 ug of total RNA was used for sequecning library construction and the libraries were prepared using the Truseq Stranded Ribo Zero Library Prep Kit.", "GEO Accession:GSM2037740", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP068364", null, null, "Toxin_1-Pack_1.fq.gz Toxin_1-Pack_2.fq.gz", "fastq fastq", 11256964600.0, 56284823.0, "GSM2037740 r1", "0:100 1:100", "A:2904557741;C:2723715275;G:2731673206;T:2896488406;N:529972", 100, 100, null, null, 2904557741, 2723715275, 2731673206, 2896488406, 529972, "SRX1528548", "SRS1246176", "SRA333195", "GEO", "Michael Pack, Medicine/DIgestive Diseases, University of Pennsylvania", 2, 0.88354, 0.88079, 0.10204, 0.10016, 0.76088, 0.76142, 0.61543, 0.61859, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "bulk", "bulk", null, "United States", "2016-01-12", "Larval", "Larval", "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": ["40353"], "units": {}, "query_ms": 8.602040999903693}