run_metadata: 15561

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
15561	ERR12916375	ERX12288722	ERS18989009	ERP159620	PRJEB75017	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E-MTAB-14020	Transcriptome Analysis	In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to Fulvestrant CAS 129453 61 8. Zebrafish embryos were exposed to Fulvestrant according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26		Protocols: at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.	Sample 5	SAMEA115497326	Department Ecotoxicogenomics, Fraunhofer Institute for molecular biology and applied ecology (IME)	ENA first public:2024 11 26\|INSDC center name:Department Ecotoxicogenomics Fraunhofer Institute for molecular biology and applied ecology IME\|INSDC status:public\|Submitter Id:E MTAB 14020:Sample 5\|age:96\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 14020:Sample 5\|scientific name:Danio rerio\|strain:Wild type AB\|tank:T12									mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	E MTAB 14020:Sample 5 p	Sample 5 p	mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	at the end of exposure 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep 24 homogeniser MP Biomedicals Irvine USA at 5 m/s speed for 45 seconds. Zebrafish embryos were exposed to Fulvestrant for xxx hours according to OECD test guidelines No. 236 at 27 ± 1 °C and a light/dark cycle of 14:10 hours. three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub lethal concentrations EC10 and EC5 of Fulvestrant CAS 129453 61 8 in addition to untreated control groups. total RNA and Protein were extracted from the tissue lysate using using the NucleoSpin® RNA/Protein kit Macherey & Nagel Düren Germany. according to the manufacturer's protocol. Nanodrop 2000 spectrophotometer Thermo Scientific was used to measure and normalize the obtained RNA concentrations. The quality of the extracted RNA samples was checked using RNA 6000 Nano kit in 2100 Bioanalyzer System Agilent Santa Clara USA. Samples were stored at 80°C. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 7 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters.		ssRNA-seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP159620	Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of Fulvestrant against untreated control groups	ENA FIRST PUBLIC:2024 11 26\|ENA LAST UPDATE:2024 11 26	NG-32227_R2070_dre_C2_fulvestrant_lib661350_10164_3_1.fastq.gz NG-32227_R2070_dre_C2_fulvestrant_lib661350_10164_3_2.fastq.gz	fastq fastq	11003883400.0	36436700.0	E MTAB 14020:NG 32227 R2070 dre C2 fulvestrant lib661350 10164 3	0:151 1:151	A:2994383363;C:2510974240;G:2552484598;T:2945879588;N:161611	151	151			2994383363	2510974240	2552484598	2945879588	161611	ERX12288722	ERS18989009	ERA29606970	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown		United Kingdom	2024-11-26	Undetermined	Embryo	Whole Organism	All anatomical structures