{"database": "metadata", "table": "run_metadata", "rows": [[40495, "SRR3203073", "SRX1612569", "SRS1321766", "SRP070923", "PRJNA313387", "Transcriptomic of \u00df diketone antibiotics on zebrafish post a 3 month DKAs exposure.", "PRJNA313387", "Other", "RNA libraries were constructed from control 6.25 and 12.5 mg/L treatment groups respectively. post DKAs exposure to 3 mpf zebrafish the whole transcriptome was determined.", null, null, "6.25 mg/L with equal weight concentrations and volumes for each of the six DKA species ofloxacin ciprofloxacin enrofloxacin doxycycline chlortetracycline and oxytetracycline was exposure to zebrafish from embryo to 90 dpf dpf", "6.25mg/L DKAs", "T11", null, "strain:AB strain|isolate:Oregon State University|breed:Danio rerio|cultivar:not applicable|ecotype:Wild type|age:3 mpf|dev stage:3 mpf|sex:pooled male and female|tissue:we performed simple anatomy of the whole fish i.e. removing gill fin and tail tissue while retaining visceral mass head spine and other nerve systems.|treatment:6.25 mg/L DKAs exposure|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "6.25 mg/L DKAs", "T11", "1", "Zebrafish in 6.25 mg/L \u03b2 diketone antibiotics treatment groupwith equal weight concentrations and volumes for ofloxacin ciprofloxacin enrofloxacin doxycycline chlortetracycline and oxytetracycline with purity of 99% except for 95% for chlortetracycline were randomly selected post DKAs exposure at 90 dpf and rinsed with phosphorous buffer solution. We performed simple anatomy of the whole fish i.e. removing gill fin and tail tissue while retaining visceral mass head spine and other nerve systems. The retained tissues were used to extract total RNA using Trizol Invitrogen Carlsbad CA USA according to the manufacturer's procedures. The quantity and purity of total RNA were analyzed by employing a Bioanalyzer 2100 and RNA 6000 Nano LabChipKit Agilent Santa Clara CA USA with RIN number >7.0. Poly A mRNA was isolated by poly T oligo attached magnetic beads Invitrogen. The purified mRNA was fragmented into small pieces by divalent cations under elevated temperature. Then the final cDNA library was produced by the reverse transcription of the cleaved RNA fragments on the basis of the mRNA Seq sample preparation kit Illumina San Diego USA and the average 300\u00b150 bp insert size was used for the paired end libraries. Finally the paired end sequencing was performed on an Illumina Hiseq2000/2500. Prior to assembly the low quality reads 1 reads containing sequencing adaptors; 2 reads containing sequencing primer; 3 nucleotide with q scores lower than 20 were removed. Next the cleaned and paired end reads were produced.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", "2000Application ReadForward11Application ReadReverse101", "SRP070923", null, null, "T11_Clean_Data1.fq.gz T11_Clean_Data2.fq.gz", "fastq fastq", 8178356500.0, 32713426.0, "T11", "0:125 1:125", "A:2135090304;C:1929011381;G:1912585084;T:2201518295;N:151436", 125, 125, null, null, 2135090304, 1929011381, 1912585084, 2201518295, 151436, "SRX1612569", "SRS1321766", "SRA359545", "School of Life Sciences", "School of Life Sciences", 2, 0.84003, 0.84827, 0.32283, 0.32402, 0.71031, 0.70502, 0.58398, 0.58631, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2016-03-15", "Adult", "Adult", "Head", "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": ["40495"], "units": {}, "query_ms": 10.934799000096973}