run_metadata: 16792
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 16792 | ERR13300236 | ERX12671098 | ERS20278808 | ERP161270 | PRJEB76780 | RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups | E-MTAB-14184 | Transcriptome Analysis | In the present study transcriptome analysis was employed to investigate the early molecular responses to Methimazole CAS 60 56 0 a thyroid peroxidase inhibitor. Zebrafish embryos were exposed to methimazole according to OECD guidelines OECD test No. 236. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina NovaSeq 6000 system Illumina Inc. San Diego USA 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 thyroid disruption specific biomarker candidates were selected based on the differential expression patterns and the biological functions investigation of the detected differentially expressed genes DEGs. | ENA FIRST PUBLIC:2024 09 01|ENA LAST UPDATE:2024 09 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 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 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 methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared. | Sample 3 | E MTAB 14184:Sample 3 | strain:AB|isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|tank:T3|age:96|developmental stage:embryo stage|geographic location country and/or sea:not collected | RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups | E MTAB 14184:Sample 3 p | Sample 3 p | RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole 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 1 min. Zebrafish embryos were exposed to Methimazole CAS 60 56 0 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 methimazole 80 and 160 mg/L in addition to untreated control groups. At the end of exposure time 96 hours RNA was extracted from 10 embryos using a NucleoSpin RNA/Protein kit Macherey Nagel Düren Germany. RNA libraries were prepared by the Eurofins Genomics Germany GmbH from RNA extracts with RNA integrity number RIN values > 9 using polyA RNA purification followed by fragmentation. random primed strand specific cDNA libraries were then prepared. | ssRNA-seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP161270 | Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Methimazole against untreated control groups | ENA FIRST PUBLIC:2024 09 01|ENA LAST UPDATE:2024 09 01 | NG-31767_R1980_dre_C2_metimazole_lib648387_10134_2_1.fastq.gz NG-31767_R1980_dre_C2_metimazole_lib648387_10134_2_2.fastq.gz | fastq fastq | 10327728050.0 | 34197775.0 | E MTAB 14184:NG 31767 R1980 dre C2 metimazole lib648387 10134 2 | 0:151 1:151 | A:2799291910;C:2358529731;G:2393199259;T:2776615639;N:91511 | 151 | 151 | 2799291910 | 2358529731 | 2393199259 | 2776615639 | 91511 | ERX12671098 | ERS20278808 | ERA30642702 | 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 | 2024-09-01 | Larval | Larval | Whole Organism | All anatomical structures |