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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
15572 ERR12916385 ERX12288732 ERS18989115 ERP159621 PRJEB75018 mRNA Seq of Danio rerio exposed to different concentrations of 17ß estradiol against untreated control groups E-MTAB-14022 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to 17ß estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17ß estradiol 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 17β estradiol 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 17β estradiol CAS 50 28 2 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 6 SAMEA115497432 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 14022:Sample 6|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14022:Sample 6|scientific name:Danio rerio|strain:Wild type AB|tank:T18                 mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups E MTAB 14022:Sample 6 p Sample 6 p mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol 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 17β estradiol 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 17β estradiol CAS 50 28 2 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   ERP159621 Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of 17β estradiol against untreated control groups ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26 NG-32544_R2131_dre_C3_estradiol_lib672210_10184_1_1.fastq.gz NG-32544_R2131_dre_C3_estradiol_lib672210_10184_1_2.fastq.gz fastq fastq 13579439362.0 44965031.0 E MTAB 14022:NG 32544 R2131 dre C3 estradiol lib672210 10184 1 0:151 1:151 A:3748627643;C:3057631445;G:3066968241;T:3705917099;N:294934 151 151     3748627643 3057631445 3066968241 3705917099 294934 ERX12288732 ERS18989115 ERA29607067 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