{"database": "metadata", "table": "run_metadata", "rows": [[56309, "SRR10916843", "SRX7584160", "SRS6018088", "SRP243451", "PRJNA602305", "Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.", "GSE143945", "Transcriptome Analysis", "Polycyclic aromatic hydrocarbons PAHs can alter gene expression by acting through the aryl hydrocarbon receptor AHR. In a previous phenotypic screen of over 120 PAHs  we identified four PAHs that induce an ectopic caudal fin called X fin in larval zebrafish: benzo[k]fluoranthene BkF  dibenzo[b k]fluoranthene  dibenzo[a h]anthracene  and benzo[j]fluoranthene. We investigated several plausible mechanisms of X fin formation using the most potent X fin inducer  BkF. The X fin phenotype was dependent on the AHR paralog Ahr2  and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue  where the phenotype was manifest  were generated for animals exposed to 1% DMSO control or 12 \u00b5M BkF. Four time points of X fin development were considered for transcriptomics: prior to visual emergence of X fin 48 hpf  during manifestation of disrupted caudal fin fold development 60 hpf and 72 hpf  and post emergence of X fin 96 hpf. Overall design: RNA profiles of larval zebrafish trunk tissue at 48  60  72  and 96 hpf  from animals exposed to either 1% DMSO or 12 \u00b5M benzo[k]fluoranthene  were generated using Illumina HiSeq 2500 with 100 bp single end reads. There were n = 50 per bioreplicate and four bioreplcates per condition  totaling 32 raw samples. Each processed sample consists of mean normalized counts from four raw data files  totaling eight processed samples.", null, "pubmed:32384158", null, "BkF 72 hpf", "GSM4277145", null, "tissue:Distal trunk tissue|developmental stage:72 hpf|treatment:12 \u03bcM Benzo[k]fluoranthene", "BkF 72 hpf", "Base calling was performed using the Illumina HiSeq 2500 system. Sequences were filtered according to Phred scores and analyzed for quality using FastQC. Sequences were trimmed using Trimmomatic. Reads were aligned with Salmon using its quasi mapping alignment method. Transcript abundances were aggregated to gene level counts using tximport. Normalized counts were generated using DESeq2. Genome build: Zv9 Supplementary files format and content: Tab delimited text files contain mean normalized counts respective to the indicated condition.", "Distal trunk tissue", "Static chemical exposures 1% DMSO or 12 \u03bcM BkF final concentrations started at 6 hpf 8 hpf and were performed using a Hewlett Packard D500e chemical dispenser. post covering with parafilm and foil  plates were placed on an automated shaker overnight at 28.5\u02daC.", "Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.", "Tropical 5D wildtype zebrafish embryos were dechorionated at 4 hpf using pronase. At 6 hpf  they were placed into 96 well plates with 100 \u03bcL E2 embryo medium per well. Following the chemical exposure procedure  wells were covered in parafilm and animals were maintained in the dark at 28.5\u02daC.", "developmental stage:72 hpf|treatment:12 \u03bcM Benzo[k]fluoranthene", "GSM4277145", "GSM4277145: BkF 72 hpf; Danio rerio; RNA Seq", "GSM4277145", null, "1", "Trunk tissue was isolated by resection at the pigment gap near the caudal peduncle which fully captured the ectopic fin region. Total RNA was isolated from fresh samples using the Zymo Direct zol RNA MiniPrep Kit and extracted following the manufacturer's standard protocol. Samples were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.", "GEO Accession:GSM4277145", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP243451", null, null, "E1-41_AGTCAA_L001_R1_001.fastq.gz", "fastq", 2601135012.0, 25753812.0, "GSM4277145 r3", "0:101 1:0", "A:650835031;C:615158716;G:595000672;T:739001381;N:1139212", 101, 0, null, null, 650835031, 615158716, 595000672, 739001381, 1139212, "SRX7584160", "SRS6018088", "SRA1028878", "GEO", "Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University", 1, 0.94866, null, 0.07141, null, 0.68887, null, 0.48668, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2020-01-20", "Larval", "Larval", "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": ["56309"], "units": {}, "query_ms": 9.029241000462207}