run_metadata: 10301

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
10301	ERR7132852	ERX6700290	ERS8071614	ERP132573	PRJEB48231	RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs	E-MTAB-11086	Transcriptome Analysis	RNA seq of wild type Tüpfel long fin TLF zebrafish embryos developmentally exposed to three addictive drugs 5 µM nicotine 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples 6 samples per drug plus 6 control samples represents RNA from a pool of seven 5 dpf zebrafish embryos exposed to the drug between 1 dpf and 5 dpf.	ENA FIRST PUBLIC:2022 01 24\|ENA LAST UPDATE:2022 01 24		Protocols: Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.	Cnt 2	SAMEA10418770	Cambridge Institute of Therapeutic Immunology & Infectious Disease	ENA first public:2022 01 24\|ENA last update:2022 01 24\|External Id:SAMEA10418770\|INSDC center alias:Cambridge Institute of Therapeutic Immunology & Infectious Disease\|INSDC center name:Cambridge Institute of Therapeutic Immunology & Infectious Disease\|INSDC first public:2022 01 24T16:27:32Z\|INSDC last update:2022 01 24T16:27:32Z\|INSDC status:public\|Submitter Id:E MTAB 11086:Cnt 2\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval day 5\|genotype:wild type genotype\|individual:pool of 7 embryos\|organism part:whole organism\|replicate:2\|sample name:E MTAB 11086:Cnt 2\|sex:not available\|strain:Tüpfel long fin TLF									Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to 3 addictive drugs	E MTAB 11086:Cnt 2 p	Cnt 2 p	RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs	Zebrafish embryos were exposed to a drug from xxx dpf ttwo xxx dpf and at the end of the exposure period larvae were collected as 6 pools of 7 embryos per condition for RNA extraction. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was removed without xxx the beads. Whilst still on the magnet beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalogue number M0303L. Illumina TruSeq Stranded mRNA Sample Prep Kit.	Experimental Factor: compound:n1	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP132573	Illumina NovaSeq 6000 paired end sequencing; RNA seq of wild type zebrafish embryos developmentally exposed to three addictive drugs	ENA FIRST PUBLIC:2022 01 24\|ENA LAST UPDATE:2022 01 24	SLX-19351.E11.HMLG7DRXX.s_2.r_1.fq.gz SLX-19351.E11.HMLG7DRXX.s_2.r_2.fq.gz	fastq fastq	2248468400.0	22484684.0	E MTAB 11086:SLX 19351.E11.HMLG7DRXX.s 2.r	0:50 1:50	A:601914808;C:521501189;G:527610060;T:597380501;N:61842	50	50			601914808	521501189	527610060	597380501	61842	ERX6700290	ERS8071614	ERA6757821	Cambridge Institute of Therapeutic Immunology & Infectious Disease\|European Nucleotide Archive	Cambridge Institute of Therapeutic Immunology & Infectious Disease\|European Nucleotide Archive	2	0.94347	0.94939	0.11234	0.10984	0.66689	0.66342	0.46711	0.46831	50	50	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown		United Kingdom	2022-01-24	Larval	Larval	Embryo Imprecise	All anatomical structures