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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
19127 ERR13769862 ERX13170663 ERS21155825 ERP165025 PRJEB81170 mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups E-MTAB-14534 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to epoxiconazole CAS 133855 98 8. Zebrafish embryos were exposed to epoxiconazole 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 selected based on the differential expression patterns and the biological functions investigation of the detected DEGs. ENA FIRST PUBLIC:2025 04 30|ENA LAST UPDATE:2025 04 30   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 epoxiconazole 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 of epoxiconazole CAS 133855 98 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 from RNA extracts with RNA integrity number RIN values > 8.5 using polyA RNA purification followed by fragmentation. Using reverse transcription cDNA libraries was produced from mRNA fragments and ligated to the adapters. Sample 6 SAMEA116134543 Fraunhofer Institute for Molecular Biology and Applied Ecology (IME) ENA first public:2025 04 30|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology IME|INSDC status:public|Submitter Id:E MTAB 14534:Sample 6|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14534:Sample 6|scientific name:Danio rerio|strain:AB|tank:19                 mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups E MTAB 14534:Sample 6 p Sample 6 p mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole 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 epoxiconazole 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 of epoxiconazole CAS 133855 98 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 from RNA extracts with RNA integrity number RIN values > 8.5 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   ERP165025 Illumina NovaSeq 6000 paired end sequencing; mRNA Seq of Danio rerio exposed to different concentrations of fungicide epoxiconazole against untreated control groups ENA FIRST PUBLIC:2025 04 30|ENA LAST UPDATE:2025 04 30 NG-A0241_R2355_dre_C3_Epoxyconazole_1.fastq.gz NG-A0241_R2355_dre_C3_Epoxyconazole_2.fastq.gz fastq fastq 7679419075.0 25506967.0 E MTAB 14534:NG A0241 R2355 dre C3 Epoxyconazole 0:150.54 1:150.54 A:2028698396;C:1826869096;G:1730945755;T:2092842481;N:63347 150 150     2028698396 1826869096 1730945755 2092842481 63347 ERX13170663 ERS21155825 ERA30873013 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 2025-04-30 Undetermined Embryo Whole Organism All anatomical structures