run_metadata: 11843
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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| 11843 | ERR11872228 | ERX11269670 | ERS16284437 | ERP150460 | PRJEB65331 | mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups | E-MTAB-13270 | Transcriptome Analysis | In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee FRAC classification. Zebrafish embryos were exposed to metalaxyl 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:2024 01 01|ENA LAST UPDATE:2024 01 01 | 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 metalaxyl 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 metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. 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 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 2 | SAMEA114295328 | Fraunhofer Institute for Molecular Biology and Aplied Ecology (IME) | ENA FIRST PUBLIC:2024 01 01T01:03:26Z|ENA LAST UPDATE:2024 01 01T01:03:26Z|External Id:SAMEA114295328|INSDC center name:Fraunhofer Institute for Molecular Biology and Aplied Ecology IME|INSDC first public:2024 01 01T01:03:26Z|INSDC last update:2024 01 01T01:03:26Z|INSDC status:public|Submitter Id:E MTAB 13270:Sample 2|age:96|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13270:Sample 2|scientific name:Danio rerio|strain:AB|tank:T6 | mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups | E MTAB 13270:Sample 2 s | Sample 2 s | mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl 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 metalaxyl 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 metalaxyl high exposure and low exposure concentrations in addition to untreated control groups. 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 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 | ERP150460 | Illumina HiSeq 4000 sequencing; mRNA Seq of Danio rerio exposed to different concentrations of the fungicide metalaxyl against untreated control groups | ENA FIRST PUBLIC:2024 01 01|ENA LAST UPDATE:2024 01 01 | p1201s1-R1716-dre-C2-metalaxyl_Eilebrecht.fastq.gz | fastq | 2700642168.0 | 53433052.0 | E MTAB 13270:Sample 2 | 0:50.54 | A:669595678;C:619368901;G:590427891;T:819827582;N:1422116 | 50 | 669595678 | 619368901 | 590427891 | 819827582 | 1422116 | ERX11269670 | ERS16284437 | ERA26965713 | 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 | 2024-01-01 | Undetermined | Embryo | Whole Organism | All anatomical structures |