run_metadata: 56332

This data as json

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
56332	SRR10916818	SRX7584154	SRS6018082	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 µM 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 µM 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.		pubmed:32384158		Control 48 hpf	GSM4277139		tissue:Distal trunk tissue\|developmental stage:48 hpf\|treatment:1% DMSO	Control 48 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 μM 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˚C.	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 μL 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˚C.	developmental stage:48 hpf\|treatment:1% DMSO	GSM4277139	GSM4277139: Control 48 hpf; Danio rerio; RNA Seq	GSM4277139		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:GSM4277139	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP243451			D1-48_CTTGTA_L001_R1_001.fastq.gz	fastq	2492562638.0	24678838.0	GSM4277139 r2	0:101 1:0	A:614317033;C:596890437;G:569548715;T:710717116;N:1089337	101	0			614317033	596890437	569548715	710717116	1089337	SRX7584154	SRS6018082	SRA1028878	GEO	Tanguay Lab, Environmental and Molecular Toxicology, Oregon State University	1	0.95109		0.06997		0.69635		0.459		101		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		United States	2020-01-20	Hatching	Embryo	Trunk	Surface Structure