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18 rows where devstage_curation_coarse = "Larval" and experiment.library_strategy = "ssRNA-seq"

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tissue_curation_coarse 1

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

  • ssRNA-seq · 18 ✖

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

devstage_curation_coarse 1

  • Larval · 18 ✖

devstage_curation 1

Link 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
16791 16791 ERR13300240 ERX12671102 ERS20278812 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 7 E MTAB 14184:Sample 7   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:T12|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 7 p Sample 7 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_R1986_dre_nc_metimazole_lib648391_10131_3_1.fastq.gz NG-31767_R1986_dre_nc_metimazole_lib648391_10131_3_2.fastq.gz fastq fastq 11260667356.0 37286978.0 E MTAB 14184:NG 31767 R1986 dre nc metimazole lib648391 10131 3 0:151 1:151 A:3081176852;C:2552857390;G:2580624774;T:3045559228;N:449112 151 151     3081176852 2552857390 2580624774 3045559228 449112 ERX12671102 ERS20278812 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
16792 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
16793 16793 ERR13300237 ERX12671099 ERS20278809 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 4 E MTAB 14184:Sample 4   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:T6|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 4 p Sample 4 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_R1982_dre_nc_metimazole_lib648388_10131_3_1.fastq.gz NG-31767_R1982_dre_nc_metimazole_lib648388_10131_3_2.fastq.gz fastq fastq 12475825058.0 41310679.0 E MTAB 14184:NG 31767 R1982 dre nc metimazole lib648388 10131 3 0:151 1:151 A:3409097477;C:2831943866;G:2867531242;T:3366748070;N:504403 151 151     3409097477 2831943866 2867531242 3366748070 504403 ERX12671099 ERS20278809 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
16794 16794 ERR13300235 ERX12671097 ERS20278807 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 2 E MTAB 14184:Sample 2   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 2 p Sample 2 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_R1979_dre_C1_metimazole_lib648386_10131_3_1.fastq.gz NG-31767_R1979_dre_C1_metimazole_lib648386_10131_3_2.fastq.gz fastq fastq 12056393264.0 39921832.0 E MTAB 14184:NG 31767 R1979 dre C1 metimazole lib648386 10131 3 0:151 1:151 A:3284811921;C:2746509095;G:2779390635;T:3245201332;N:480281 151 151     3284811921 2746509095 2779390635 3245201332 480281 ERX12671097 ERS20278807 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
16795 16795 ERR13300234 ERX12671096 ERS20278806 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 1 E MTAB 14184:Sample 1   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 1 p Sample 1 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_R1978_dre_nc_metimazole_lib648385_10131_3_1.fastq.gz NG-31767_R1978_dre_nc_metimazole_lib648385_10131_3_2.fastq.gz fastq fastq 13764936218.0 45579259.0 E MTAB 14184:NG 31767 R1978 dre nc metimazole lib648385 10131 3 0:151 1:151 A:3758304493;C:3129474937;G:3161322918;T:3715288378;N:545492 151 151     3758304493 3129474937 3161322918 3715288378 545492 ERX12671096 ERS20278806 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
16796 16796 ERR13300242 ERX12671104 ERS20278814 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 9 E MTAB 14184:Sample 9   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:T12|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 9 p Sample 9 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_R1988_dre_C2_metimazole_lib648393_10134_2_1.fastq.gz NG-31767_R1988_dre_C2_metimazole_lib648393_10134_2_2.fastq.gz fastq fastq 13519918182.0 44767941.0 E MTAB 14184:NG 31767 R1988 dre C2 metimazole lib648393 10134 2 0:151 1:151 A:3699694563;C:3061675737;G:3096126907;T:3662301667;N:119308 151 151     3699694563 3061675737 3096126907 3662301667 119308 ERX12671104 ERS20278814 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
16797 16797 ERR13300239 ERX12671101 ERS20278811 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 6 E MTAB 14184:Sample 6   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:T6|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 6 p Sample 6 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_R1984_dre_C2_metimazole_lib648390_10131_3_1.fastq.gz NG-31767_R1984_dre_C2_metimazole_lib648390_10131_3_2.fastq.gz fastq fastq 11682386498.0 38683399.0 E MTAB 14184:NG 31767 R1984 dre C2 metimazole lib648390 10131 3 0:151 1:151 A:3197033917;C:2653110640;G:2674567052;T:3157209187;N:465702 151 151     3197033917 2653110640 2674567052 3157209187 465702 ERX12671101 ERS20278811 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
16798 16798 ERR13300241 ERX12671103 ERS20278813 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 8 E MTAB 14184:Sample 8   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:T12|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 8 p Sample 8 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_R1987_dre_C1_metimazole_lib648392_10134_2_1.fastq.gz NG-31767_R1987_dre_C1_metimazole_lib648392_10134_2_2.fastq.gz fastq fastq 14249559544.0 47183972.0 E MTAB 14184:NG 31767 R1987 dre C1 metimazole lib648392 10134 2 0:151 1:151 A:3912991191;C:3212312586;G:3257466757;T:3866663511;N:125499 151 151     3912991191 3212312586 3257466757 3866663511 125499 ERX12671103 ERS20278813 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
16799 16799 ERR13300238 ERX12671100 ERS20278810 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 5 E MTAB 14184:Sample 5   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:T6|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 5 p Sample 5 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_R1983_dre_C1_metimazole_lib648389_10131_3_1.fastq.gz NG-31767_R1983_dre_C1_metimazole_lib648389_10131_3_2.fastq.gz fastq fastq 12432697344.0 41167872.0 E MTAB 14184:NG 31767 R1983 dre C1 metimazole lib648389 10131 3 0:151 1:151 A:3393249603;C:2829226513;G:2854931342;T:3354793579;N:496307 151 151     3393249603 2829226513 2854931342 3354793579 496307 ERX12671100 ERS20278810 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
16800 16800 ERR13301113 ERX12671975 ERS20279263 ERP161271 PRJEB76781 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups E-MTAB-14185 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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 9 E MTAB 14185:Sample 9   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:T12|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 Iopanoic acid against untreated control groups E MTAB 14185:Sample 9 p Sample 9 p RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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   ERP161271 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups ENA FIRST PUBLIC:2024 09 01|ENA LAST UPDATE:2024 09 01 NG-31767_R1977_dre_C3_iopanicacid_lib648384_10134_2_1.fastq.gz NG-31767_R1977_dre_C3_iopanicacid_lib648384_10134_2_2.fastq.gz fastq fastq 14923903196.0 49416898.0 E MTAB 14185:NG 31767 R1977 dre C3 iopanicacid lib648384 10134 2 0:151 1:151 A:4052219773;C:3416033337;G:3452773871;T:4002745593;N:130622 151 151     4052219773 3416033337 3452773871 4002745593 130622 ERX12671975 ERS20279263 ERA30642739 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
16801 16801 ERR13301105 ERX12671967 ERS20279255 ERP161271 PRJEB76781 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups E-MTAB-14185 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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 1 E MTAB 14185:Sample 1   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 Iopanoic acid against untreated control groups E MTAB 14185:Sample 1 p Sample 1 p RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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   ERP161271 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups ENA FIRST PUBLIC:2024 09 01|ENA LAST UPDATE:2024 09 01 NG-31767_R1966_dre_nc_iopanicacid_lib648376_10134_2_1.fastq.gz NG-31767_R1966_dre_nc_iopanicacid_lib648376_10134_2_2.fastq.gz fastq fastq 14323093524.0 47427462.0 E MTAB 14185:NG 31767 R1966 dre nc iopanicacid lib648376 10134 2 0:151 1:151 A:3915028461;C:3251486078;G:3281494434;T:3874958216;N:126335 151 151     3915028461 3251486078 3281494434 3874958216 126335 ERX12671967 ERS20279255 ERA30642739 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
16802 16802 ERR13301112 ERX12671974 ERS20279262 ERP161271 PRJEB76781 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups E-MTAB-14185 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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 8 E MTAB 14185:Sample 8   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:T12|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 Iopanoic acid against untreated control groups E MTAB 14185:Sample 8 p Sample 8 p RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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   ERP161271 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups ENA FIRST PUBLIC:2024 09 01|ENA LAST UPDATE:2024 09 01 NG-31767_R1976_dre_C2_iopanicacid_lib648383_10131_3_1.fastq.gz NG-31767_R1976_dre_C2_iopanicacid_lib648383_10131_3_2.fastq.gz fastq fastq 10961479882.0 36296291.0 E MTAB 14185:NG 31767 R1976 dre C2 iopanicacid lib648383 10131 3 0:151 1:151 A:2983032221;C:2502602193;G:2529591204;T:2945818101;N:436163 151 151     2983032221 2502602193 2529591204 2945818101 436163 ERX12671974 ERS20279262 ERA30642739 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
16803 16803 ERR13301110 ERX12671972 ERS20279260 ERP161271 PRJEB76781 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups E-MTAB-14185 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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 6 E MTAB 14185:Sample 6   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:T6|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 Iopanoic acid against untreated control groups E MTAB 14185:Sample 6 p Sample 6 p RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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   ERP161271 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups ENA FIRST PUBLIC:2024 09 01|ENA LAST UPDATE:2024 09 01 NG-31767_R1973_dre_C3_iopanicacid_lib648381_10134_2_1.fastq.gz NG-31767_R1973_dre_C3_iopanicacid_lib648381_10134_2_2.fastq.gz fastq fastq 11098074784.0 36748592.0 E MTAB 14185:NG 31767 R1973 dre C3 iopanicacid lib648381 10134 2 0:151 1:151 A:3011128450;C:2542381325;G:2563170447;T:2981297586;N:96976 151 151     3011128450 2542381325 2563170447 2981297586 96976 ERX12671972 ERS20279260 ERA30642739 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
16804 16804 ERR13301109 ERX12671971 ERS20279259 ERP161271 PRJEB76781 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups E-MTAB-14185 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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 5 E MTAB 14185:Sample 5   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:T6|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 Iopanoic acid against untreated control groups E MTAB 14185:Sample 5 p Sample 5 p RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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   ERP161271 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups ENA FIRST PUBLIC:2024 09 01|ENA LAST UPDATE:2024 09 01 NG-31767_R1972_dre_C2_iopanicacid_lib648380_10131_3_1.fastq.gz NG-31767_R1972_dre_C2_iopanicacid_lib648380_10131_3_2.fastq.gz fastq fastq 13552628708.0 44876254.0 E MTAB 14185:NG 31767 R1972 dre C2 iopanicacid lib648380 10131 3 0:151 1:151 A:3683544144;C:3104040164;G:3130331394;T:3634170005;N:543001 151 151     3683544144 3104040164 3130331394 3634170005 543001 ERX12671971 ERS20279259 ERA30642739 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
16805 16805 ERR13301111 ERX12671973 ERS20279261 ERP161271 PRJEB76781 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups E-MTAB-14185 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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 7 E MTAB 14185:Sample 7   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:T12|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 Iopanoic acid against untreated control groups E MTAB 14185:Sample 7 p Sample 7 p RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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   ERP161271 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups ENA FIRST PUBLIC:2024 09 01|ENA LAST UPDATE:2024 09 01 NG-31767_R1974_dre_nc_iopanicacid_lib648382_10134_2_1.fastq.gz NG-31767_R1974_dre_nc_iopanicacid_lib648382_10134_2_2.fastq.gz fastq fastq 15020718054.0 49737477.0 E MTAB 14185:NG 31767 R1974 dre nc iopanicacid lib648382 10134 2 0:151 1:151 A:4067785748;C:3448087461;G:3475467669;T:4029245322;N:131854 151 151     4067785748 3448087461 3475467669 4029245322 131854 ERX12671973 ERS20279261 ERA30642739 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
16806 16806 ERR13301106 ERX12671968 ERS20279256 ERP161271 PRJEB76781 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups E-MTAB-14185 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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 2 E MTAB 14185:Sample 2   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 Iopanoic acid against untreated control groups E MTAB 14185:Sample 2 p Sample 2 p RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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   ERP161271 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups ENA FIRST PUBLIC:2024 09 01|ENA LAST UPDATE:2024 09 01 NG-31767_R1968_dre_C2_iopanicacid_lib648377_10131_3_1.fastq.gz NG-31767_R1968_dre_C2_iopanicacid_lib648377_10131_3_2.fastq.gz fastq fastq 11754494132.0 38922166.0 E MTAB 14185:NG 31767 R1968 dre C2 iopanicacid lib648377 10131 3 0:151 1:151 A:3200002137;C:2683120669;G:2711161374;T:3159741610;N:468342 151 151     3200002137 2683120669 2711161374 3159741610 468342 ERX12671968 ERS20279256 ERA30642739 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
16807 16807 ERR13301107 ERX12671969 ERS20279257 ERP161271 PRJEB76781 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups E-MTAB-14185 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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 14185: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 Iopanoic acid against untreated control groups E MTAB 14185:Sample 3 p Sample 3 p RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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   ERP161271 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups ENA FIRST PUBLIC:2024 09 01|ENA LAST UPDATE:2024 09 01 NG-31767_R1969_dre_C3_iopanicacid_lib648378_10134_2_1.fastq.gz NG-31767_R1969_dre_C3_iopanicacid_lib648378_10134_2_2.fastq.gz fastq fastq 12466152904.0 41278652.0 E MTAB 14185:NG 31767 R1969 dre C3 iopanicacid lib648378 10134 2 0:151 1:151 A:3383255890;C:2853477802;G:2880177719;T:3349132410;N:109083 151 151     3383255890 2853477802 2880177719 3349132410 109083 ERX12671969 ERS20279257 ERA30642739 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
16808 16808 ERR13301108 ERX12671970 ERS20279258 ERP161271 PRJEB76781 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups E-MTAB-14185 Transcriptome Analysis In the present study transcriptome analysis was employed to investigate the early molecular responses to Iopanoic acid CAS 96 83 3 a deiodinase inhibitor. Zebrafish embryos were exposed to Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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 4 E MTAB 14185:Sample 4   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:T6|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 Iopanoic acid against untreated control groups E MTAB 14185:Sample 4 p Sample 4 p RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid 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 Iopanoic acid CAS 96 83 3 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 6.25 and 12.5 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   ERP161271 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Iopanoic acid against untreated control groups ENA FIRST PUBLIC:2024 09 01|ENA LAST UPDATE:2024 09 01 NG-31767_R1970_dre_nc_iopanicacid_lib648379_10134_2_1.fastq.gz NG-31767_R1970_dre_nc_iopanicacid_lib648379_10134_2_2.fastq.gz fastq fastq 12166326096.0 40285848.0 E MTAB 14185:NG 31767 R1970 dre nc iopanicacid lib648379 10134 2 0:151 1:151 A:3269774977;C:2810343720;G:2853693327;T:3232407966;N:106106 151 151     3269774977 2810343720 2853693327 3232407966 106106 ERX12671970 ERS20279258 ERA30642739 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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;