run_metadata: 19140
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 |
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| 19140 | ERR13769875 | ERX13170676 | ERS21156063 | ERP165027 | PRJEB81172 | mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups | E-MTAB-14536 | Transcriptome Analysis | In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to difenoconazole 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 HiSeq 4000 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: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 difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 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 difenoconazole high exposure and low exposure concentrations 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 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA | Sample 1 | SAMEA116134556 | 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 14536:Sample 1|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 14536:Sample 1|scientific name:Danio rerio|strain:AB|tank:T7 | mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups | E MTAB 14536:Sample 1 s | Sample 1 s | mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole 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 difenoconazole for xxx hours according to OECD test guidelines No. 236 at 26 ± 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 difenoconazole high exposure and low exposure concentrations 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 using polyA RNA purification and the TruSeq RNA Library Prep Kit v2 Illumina San Diego USA | RNA-Seq | TRANSCRIPTOMIC | PolyA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | ERP165027 | Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide difenoconazole against untreated control groups | ENA FIRST PUBLIC:2025 04 30|ENA LAST UPDATE:2025 04 30 | p1067sR1426.fastq.gz | fastq | 1044742413.0 | 20762139.0 | E MTAB 14536:Sample 1 | 0:50.32 | A:250471042;C:265283643;G:251710894;T:266877610;N:10399224 | 50 | 250471042 | 265283643 | 251710894 | 266877610 | 10399224 | ERX13170676 | ERS21156063 | ERA30873015 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | unknown | unknown | United Kingdom | 2025-04-30 | Undetermined | Embryo | Whole Organism | All anatomical structures |