{"database": "metadata", "table": "run_metadata", "rows": [[69998, "SRR19264380", "SRX15324804", "SRS13053420", "SRP375841", "PRJNA839281", "Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene", "GSE203258", "Transcriptome Analysis", "Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish", null, null, null, "RNA   Retene 20 \u00b5M   Replicate 4", "GSM6165405", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 20 \u00b5M|FISH strain:Tropical 5D", "RNA   Retene 20 \u00b5M   Replicate 4", "Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11", "Whole zebrafish larvae", "Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 \u00b5M", "48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.", "Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.", "timepoint:48 hpf 20 \u00b5M|FISH strain:Tropical 5D", "GSM6165405", "GSM6165405: RNA   Retene 20 \u00b5M   Replicate 4; Danio rerio; RNA Seq", "GSM6165405 r1", "GSM6165405", "1", "48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "Ret28_2.fq Ret28_1.fq", "fastq fastq", 4605153200.0, 46051532.0, "GSM6165405 r1", "0:100 1:100", "A:1237345826;C:1045225477;G:1091001207;T:1231580690;N:0", 100, 100, null, null, 1237345826, 1045225477, 1091001207, 1231580690, 0, "SRX15324804", "SRS13053420", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.92128, null, 0.10244, null, 0.70524, null, 0.49879, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-05-18", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"]], "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": ["69998"], "units": {}, "query_ms": 13.964997997391038}