{"database": "metadata", "table": "run_metadata", "rows": [[53656, "SRR10010337", "SRX6748601", "SRS5298717", "SRP219014", "PRJNA561212", "RNA Seq of nr5a1a and nr5a1b mutant zebrafish", "PRJNA561212", "Transcriptome Analysis", "Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed  strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM  and multiplexed. Prior to sequencing  wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.", null, null, null, null, "35dpf nr5a1a nr5a1b", null, "strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab  University of Oregon|genotype:nr5a1a  /  ; nr5a1b  / |BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 35dpf nr5a1a nr5a1b double mutant 10", "35dpf nr5a1a nr5a1b double mutant 10", "35dpf nr5a1a nr5a1b double mutant 10", "Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP219014", null, null, "nr5a1ab35dmut-10_combined_R1.fq.gz nr5a1ab35dmut-10_combined_R2.fq.gz", "fastq fastq", 3016366034.0, 9987967.0, "nr5a1ab35dmut 10 combined R1.fq.gz", "0:151 1:151", "A:752733986;C:720025699;G:731849549;T:811247600;N:509200", 151, 151, null, null, 752733986, 720025699, 731849549, 811247600, 509200, "SRX6748601", "SRS5298717", "SRA946180", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.90615, 0.91707, 0.11046, 0.07981, 0.74651, 0.74966, 0.49676, 0.60165, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-08-21", "Juvenile", "Juvenile", "Trunk", "Surface Structure"]], "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": ["53656"], "units": {}, "query_ms": 13.30484299978707}