run_metadata: 5805

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
5805	ERR1698342	ERX1767850	ERS1417524	ERP018188	PRJEB16335	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17a ethinylestradiol	E-MTAB-5173	Transcriptome Analysis	17a ethinylestradiol EE2 is a synthetic estrogen commonly used as an active substance in oral contraceptives. It is frequently found in waste water effluent and raise concern due to its persistent nature. EE2 binds to estrogen receptors with similar affinity to oestradiol and acts as one of the most potent hormone mimics found in the environment. Estrogen is involved in many aspects of the development of the neuroendocrine system influencing both brain structure and behavior. We and others have reported a significant effect on non reproductive behaviors in adult fish and in recent studies we found that developmental exposure to EE2 resulted in an anxiogenic phenotype as adults even post a long remediation period. In this study we aim to study possible mechanisms behind the behavior alterations of zebrafish developmentally exposed to EE2 by sequencing the whole brain transcriptome. Zebrafish embryos were exposed to 0 2.14 and 7.34 ng/L EE2 from 1 day to 80 dpf post the exposure period a remediation period of 120 days followed before the fish were sampled. 3 male brains from the control group 0 ng/L and the 2.14 ng/L group were sampled and 3 female brains from the control group 0 ng/L and 7.34 ng/L were sampled.	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2016 10 19\|ArrayExpress:E MTAB 5173		Protocols: RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	IonXpressRNA 002 up 058 2	SAMEA4518345	School of Natural Science, Technology and Environmental Studies Sodertorn University	ENA first public:2017 10 02\|ENA last update:2016 10 19\|External Id:SAMEA4518345\|INSDC center alias:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC center name:School of Natural Science Technology and Environmental Studies Sodertorn University\|INSDC first public:2017 10 02T17:05:16Z\|INSDC last update:2016 10 19T13:53:59Z\|INSDC status:public\|Submitter Id:E MTAB 5173:IonXpressRNA 002 up 058 2\|age:200\|broker name:ArrayExpress\|common name:zebrafish\|organism part:brain\|sample name:E MTAB 5173:IonXpressRNA 002 up 058 2\|sex:female									Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	E MTAB 5173:IonXpressRNA 002 up 058 2 s	IonXpressRNA 002 up 058 2 s	RNA seq of the zebrafish danio rerio brain post developmental exposure to 17α ethinylestradiol	RNA extraction Whole brains homogenized in TriReagent according to the manufacturer 0.8 ml/sample Sigma Aldrich Germany EE2 exposure. Fish exposed to 0 2.14 or 7.34 ng/L EE2 for 80 days starting 1 dpf Ion Whole transcriptome analysis kit on RiboZero eukaryote depleted total RNA	Experimental Factor: female:sex\|Experimental Factor: n1:compound	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP018188	Ion Torrent Proton sequencing; RNA seq of the zebrafish danio rerio brain post developmental exposure to 17Î± ethinylestradiol	ENA FIRST PUBLIC:2017 10 02\|ENA LAST UPDATE:2018 11 16	IonXpressRNA_002_up_058_2.fastq.gz	fastq	2679963893.0	33552723.0	E MTAB 5173:IonXpressRNA 002 up 058 2	0:79.87	A:709092431;C:635329399;G:670478210;T:665063853;N:0	79				709092431	635329399	670478210	665063853	0	ERX1767850	ERS1417524	ERA739176	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	School of Natural Science, Technology and Environmental Studies Sodertorn University\|European Nucleotide Archive	1	0.43283		0.18649		0.81178		0.52885		116		B		usable mapping rate	ion_torrent	ion_torrent	full_length	random_priming	ribozero	bulk	unknown	unknown		Sweden	2016-10-19	Pharyngula	Embryo	Brain	Nervous System