run_metadata: 10380

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
10380	ERR8058369	ERX7625090	ERS10119350	ERP134902	PRJEB50332	RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine	E-MTAB-11346	Transcriptome Analysis	To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform	ENA FIRST PUBLIC:2023 01 03\|ENA LAST UPDATE:2023 01 03		Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR	Cocaine 3	SAMEA12512746	Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.	ENA FIRST PUBLIC:2022 12 31\|ENA LAST UPDATE:2022 12 31\|External Id:SAMEA12512746\|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.\|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.\|INSDC first public:2022 12 31T00:57:45Z\|INSDC last update:2022 12 31T00:57:45Z\|INSDC status:public\|Submitter Id:E MTAB 11346:Cocaine 3\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|developmental stage:72\|genotype:wild type genotype\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11346:Cocaine 3\|strain:AB									Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine	E MTAB 11346:Cocaine 3 p	Cocaine 3 p	RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine	At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR	Experimental Factor: compound:cocaine\|Experimental Factor: dose:15	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000		ERP134902	Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine	ENA FIRST PUBLIC:2023 01 03\|ENA LAST UPDATE:2023 01 03	NG-10331_4CC_lib138516_4790_6_1.fastq.gz NG-10331_4CC_lib138516_4790_6_2.fastq.gz	fastq fastq	9574359984.0	37993492.0	E MTAB 11346:NG 10331 4CC lib138516 4790 6	0:126 1:126	A:2623103101;C:2170327733;G:2166494677;T:2613276955;N:1157518	126	126			2623103101	2170327733	2166494677	2613276955	1157518	ERX7625090	ERS10119350	ERA8439547	Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.\|European Nucleotide Archive	Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.\|European Nucleotide Archive	2	0.9366	0.93856	0.10196	0.09901	0.69018	0.69611	0.46501	0.46917	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown		Spain	2022-12-31	Larval	Larval	Whole Organism	All anatomical structures