{"database": "metadata", "table": "run_metadata", "rows": [[15569, "ERR12916380", "ERX12288727", "ERS18989110", "ERP159621", "PRJEB75018", "mRNA  Seq of Danio rerio exposed to different concentrations of 17\u00df 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 17\u00df estradiol CAS 50 28 2. Zebrafish embryos were exposed to 17\u00df 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", null, "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 17\u03b2 estradiol for xxx hours according to OECD test guidelines No. 236 at 27 \u00b1 1 \u00b0C 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 17\u03b2 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\u00ae RNA/Protein kit Macherey & Nagel  D\u00fcren  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\u00b0C.   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 1", "SAMEA115497427", "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 1|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 1|scientific name:Danio rerio|strain:Wild type AB|tank:T8", null, null, null, null, null, null, null, null, "mRNA  Seq of Danio rerio exposed to different concentrations of 17\u03b2 estradiol against untreated control groups", "E MTAB 14022:Sample 1 p", "Sample 1 p", "mRNA  Seq of Danio rerio exposed to different concentrations of 17\u03b2 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 17\u03b2 estradiol for xxx hours according to OECD test guidelines No. 236 at 27 \u00b1 1 \u00b0C 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 17\u03b2 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\u00ae RNA/Protein kit Macherey & Nagel  D\u00fcren  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\u00b0C.   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.", null, "ssRNA-seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP159621", "Illumina NovaSeq 6000 paired end sequencing; mRNA  Seq of Danio rerio exposed to different concentrations of 17\u00ce\u00b2 estradiol against untreated control groups", "ENA FIRST PUBLIC:2024 11 26|ENA LAST UPDATE:2024 11 26", "NG-32544_R2123_dre_nc_estradiol_lib676807_10195_2_1.fastq.gz NG-32544_R2123_dre_nc_estradiol_lib676807_10195_2_2.fastq.gz", "fastq fastq", 9678660288.0, 32048544.0, "E MTAB 14022:NG 32544 R2123 dre nc estradiol lib676807 10195 2 ", "0:151 1:151", "A:2651923654;C:2190605826;G:2231831230;T:2604055145;N:244433", 151, 151, null, null, 2651923654, 2190605826, 2231831230, 2604055145, 244433, "ERX12288727", "ERS18989110", "ERA29607067", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2024-11-26", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["15569"], "units": {}, "query_ms": 9.521854008198716}