{"database": "metadata", "table": "run_metadata", "rows": [[40496, "SRR3195594", "SRX1604653", "SRS1314385", "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, null, null, "zebrafish", 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.|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "control", "CON 01", "1", "Zebrafish in control group 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 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", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP070923", null, null, "CON_01_Clean_Data2.fq.gz CON_01_Clean_Data1.fq.gz", "fastq fastq", 8941582750.0, 35766331.0, "control", "0:125 1:125", "A:2282842470;C:2172817074;G:2169521320;T:2316254609;N:147277", 125, 125, null, null, 2282842470, 2172817074, 2169521320, 2316254609, 147277, "SRX1604653", "SRS1314385", "SRA359545", "School of Life Sciences", "School of Life Sciences", 2, 0.62865, 0.62758, 0.22408, 0.21961, 0.7525, 0.75024, 0.5332, 0.519, 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": ["40496"], "units": {}, "query_ms": 11.84857200132683}