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run_metadata

1,079 rows where experiment.library_selection = "PolyA", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Whole Organism"

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devstage_curation 8

devstage_curation_coarse 4

technology 3

experiment.library_strategy 3

experiment.platform 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Whole Organism · 1,079 ✖

experiment.library_source 1

  • TRANSCRIPTOMIC · 1,079 ✖

experiment.library_selection 1

  • PolyA · 1,079 ✖
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
7898 7898 ERR3446778 ERX3468777 ERS1806709 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 A7 SAMEA104147691 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147691|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:32Z|INSDC status:public|Submitter Id:3a44a000 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3a44a000 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934993                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#48 DN488439N:H6 Illumina sequencing of library DN488439N:H6 constructed from sample accession ERS1806709 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TTCAGCTC. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#48.cram cram 308695200.0 2057968.0 SC RUN 22829 8#48 0:75 1:75 A:81122866;C:71193244;G:71997258;T:83822324;N:559508 75 75     81122866 71193244 71997258 83822324 559508 ERX3468777 ERS1806709 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.89599 0.93164 0.14865 0.15283 0.69217 0.69759 0.50417 0.50646 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7899 7899 ERR3446777 ERX3468776 ERS1806708 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 A10 SAMEA104147690 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147690|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:32Z|INSDC status:public|Submitter Id:3a397c70 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3a397c70 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934992                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#47 DN488439N:G6 Illumina sequencing of library DN488439N:G6 constructed from sample accession ERS1806708 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TACTAGTC. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#47.cram cram 995580450.0 6637203.0 SC RUN 22829 8#47 0:75 1:75 A:262413326;C:232761029;G:232382381;T:266176133;N:1847581 75 75     262413326 232761029 232382381 266176133 1847581 ERX3468776 ERS1806708 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95746 0.96146 0.13411 0.13002 0.69954 0.70128 0.51593 0.51584 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7900 7900 ERR3446776 ERX3468775 ERS1806707 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 A5 SAMEA104147689 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147689|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:32Z|INSDC status:public|Submitter Id:3a2b4ba0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3a2b4ba0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934991                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#46 DN488439N:F6 Illumina sequencing of library DN488439N:F6 constructed from sample accession ERS1806707 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TCAGATTC. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#46.cram cram 802088550.0 5347257.0 SC RUN 22829 8#46 0:75 1:75 A:215471665;C:183766661;G:183444943;T:217939641;N:1465640 75 75     215471665 183766661 183444943 217939641 1465640 ERX3468775 ERS1806707 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95288 0.95668 0.16762 0.16588 0.68785 0.6896 0.51555 0.51471 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7901 7901 ERR3446775 ERX3468774 ERS1806706 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 E7 SAMEA104147688 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147688|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:32Z|INSDC status:public|Submitter Id:3a207630 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3a207630 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934990                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#45 DN488439N:E6 Illumina sequencing of library DN488439N:E6 constructed from sample accession ERS1806706 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TATGCCAG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#45.cram cram 895634850.0 5970899.0 SC RUN 22829 8#45 0:75 1:75 A:237133265;C:208424547;G:207465996;T:240955635;N:1655407 75 75     237133265 208424547 207465996 240955635 1655407 ERX3468774 ERS1806706 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95242 0.95616 0.148 0.14527 0.68166 0.68489 0.49334 0.49766 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7902 7902 ERR3446774 ERX3468773 ERS1806705 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 D5 SAMEA104147687 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147687|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:32Z|INSDC status:public|Submitter Id:3a15a0c0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3a15a0c0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934989                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#44 DN488439N:D6 Illumina sequencing of library DN488439N:D6 constructed from sample accession ERS1806705 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TGGCTCAG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#44.cram cram 897162300.0 5981082.0 SC RUN 22829 8#44 0:75 1:75 A:236623845;C:209590114;G:209138794;T:240168869;N:1640678 75 75     236623845 209590114 209138794 240168869 1640678 ERX3468773 ERS1806705 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95642 0.95978 0.15673 0.15393 0.68941 0.69298 0.50945 0.51331 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7903 7903 ERR3446773 ERX3468772 ERS1806704 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 B9 SAMEA104147686 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147686|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:32Z|INSDC status:public|Submitter Id:3a0acb50 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3a0acb50 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934988                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#43 DN488439N:C6 Illumina sequencing of library DN488439N:C6 constructed from sample accession ERS1806704 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TCATTGAG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#43.cram cram 1041347100.0 6942314.0 SC RUN 22829 8#43 0:75 1:75 A:275192375;C:242588569;G:242047235;T:279597410;N:1921511 75 75     275192375 242588569 242047235 279597410 1921511 ERX3468772 ERS1806704 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95538 0.95935 0.12658 0.12175 0.68527 0.68594 0.49686 0.49869 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7904 7904 ERR3446772 ERX3468771 ERS1806703 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 A9 SAMEA104147685 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147685|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:32Z|INSDC status:public|Submitter Id:39fff5e0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39fff5e0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934987                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#42 DN488439N:B6 Illumina sequencing of library DN488439N:B6 constructed from sample accession ERS1806703 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TGTATGCG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#42.cram cram 1003046550.0 6686977.0 SC RUN 22829 8#42 0:75 1:75 A:264604462;C:234287668;G:233610516;T:268704610;N:1839294 75 75     264604462 234287668 233610516 268704610 1839294 ERX3468771 ERS1806703 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.9545 0.95817 0.14837 0.14477 0.69075 0.69477 0.5059 0.50954 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7905 7905 ERR3446771 ERX3468770 ERS1806702 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 D1 SAMEA104147684 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147684|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:32Z|INSDC status:public|Submitter Id:39f52070 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39f52070 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934986                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#41 DN488439N:A6 Illumina sequencing of library DN488439N:A6 constructed from sample accession ERS1806702 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TCCAGTCG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#41.cram cram 941981400.0 6279876.0 SC RUN 22829 8#41 0:75 1:75 A:246347736;C:221993645;G:222033599;T:249879875;N:1726545 75 75     246347736 221993645 222033599 249879875 1726545 ERX3468770 ERS1806702 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95497 0.95862 0.14626 0.14366 0.68069 0.68219 0.51091 0.5108 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7906 7906 ERR3446770 ERX3468769 ERS1806701 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 F3 SAMEA104147683 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147683|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:31Z|INSDC status:public|Submitter Id:39ea4b00 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39ea4b00 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934985                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#40 DN488439N:H5 Illumina sequencing of library DN488439N:H5 constructed from sample accession ERS1806701 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TAAGTTCG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#40.cram cram 943793700.0 6291958.0 SC RUN 22829 8#40 0:75 1:75 A:248418195;C:220858029;G:220899307;T:251893736;N:1724433 75 75     248418195 220858029 220899307 251893736 1724433 ERX3468769 ERS1806701 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95501 0.95869 0.15165 0.15013 0.6858 0.68968 0.51097 0.51107 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7907 7907 ERR3446769 ERX3468768 ERS1806700 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 A12 SAMEA104147682 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147682|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:31Z|INSDC status:public|Submitter Id:39df7590 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39df7590 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934984                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#39 DN488439N:G5 Illumina sequencing of library DN488439N:G5 constructed from sample accession ERS1806700 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TCAGGAGG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#39.cram cram 1013740350.0 6758269.0 SC RUN 22829 8#39 0:75 1:75 A:272175825;C:231609775;G:230992859;T:277093551;N:1868340 75 75     272175825 231609775 230992859 277093551 1868340 ERX3468768 ERS1806700 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95017 0.95405 0.17783 0.17326 0.69374 0.69792 0.52105 0.52106 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7908 7908 ERR3446768 ERX3468767 ERS1806699 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 A8 SAMEA104147681 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147681|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:31Z|INSDC status:public|Submitter Id:39d4a020 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39d4a020 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934983                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#38 DN488439N:F5 Illumina sequencing of library DN488439N:F5 constructed from sample accession ERS1806699 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TCTCACGG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#38.cram cram 795064350.0 5300429.0 SC RUN 22829 8#38 0:75 1:75 A:213296717;C:181969652;G:181448689;T:216888172;N:1461120 75 75     213296717 181969652 181448689 216888172 1461120 ERX3468767 ERS1806699 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95132 0.955 0.15976 0.15558 0.68483 0.68828 0.50493 0.50817 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7909 7909 ERR3446767 ERX3468766 ERS1806698 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 D8 SAMEA104147680 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147680|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:31Z|INSDC status:public|Submitter Id:39c9cab0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39c9cab0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934982                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#37 DN488439N:E5 Illumina sequencing of library DN488439N:E5 constructed from sample accession ERS1806698 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TACTTCGG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#37.cram cram 977579400.0 6517196.0 SC RUN 22829 8#37 0:75 1:75 A:259910020;C:226288538;G:225374569;T:264216059;N:1790214 75 75     259910020 226288538 225374569 264216059 1790214 ERX3468766 ERS1806698 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95353 0.95725 0.15221 0.14901 0.68442 0.6873 0.48878 0.49948 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7910 7910 ERR3446766 ERX3468765 ERS1806697 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 D9 SAMEA104147679 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147679|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:31Z|INSDC status:public|Submitter Id:39bece30 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39bece30 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934981                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#36 DN488439N:D5 Illumina sequencing of library DN488439N:D5 constructed from sample accession ERS1806697 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TGAACTGG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#36.cram cram 936668850.0 6244459.0 SC RUN 22829 8#36 0:75 1:75 A:249181628;C:216639604;G:216150821;T:252967247;N:1729550 75 75     249181628 216639604 216150821 252967247 1729550 ERX3468765 ERS1806697 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95513 0.95852 0.15768 0.15381 0.68438 0.68799 0.51177 0.50632 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7911 7911 ERR3446765 ERX3468764 ERS1806696 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 C1 SAMEA104147678 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147678|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:31Z|INSDC status:public|Submitter Id:39b3f8c0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39b3f8c0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934980                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#35 DN488439N:C5 Illumina sequencing of library DN488439N:C5 constructed from sample accession ERS1806696 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TTGGTATG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#35.cram cram 975853650.0 6505691.0 SC RUN 22829 8#35 0:75 1:75 A:258866840;C:226232975;G:225877015;T:263074733;N:1802087 75 75     258866840 226232975 225877015 263074733 1802087 ERX3468764 ERS1806696 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95586 0.9586 0.14753 0.14367 0.68964 0.69345 0.50825 0.50489 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7912 7912 ERR3446764 ERX3468763 ERS1806694 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 E5 SAMEA104147676 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147676|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:39a74e90 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39a74e90 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934979                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#34 DN488439N:B5 Illumina sequencing of library DN488439N:B5 constructed from sample accession ERS1806694 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TAACGCTG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#34.cram cram 960618450.0 6404123.0 SC RUN 22829 8#34 0:75 1:75 A:252530928;C:225220073;G:224701067;T:256397819;N:1768563 75 75     252530928 225220073 224701067 256397819 1768563 ERX3468763 ERS1806694 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95621 0.95933 0.15326 0.15001 0.68278 0.68574 0.50498 0.50559 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7913 7913 ERR3446763 ERX3468762 ERS1806693 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 D11 SAMEA104147675 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147675|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:399c7920 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:399c7920 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934978                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#33 DN488439N:A5 Illumina sequencing of library DN488439N:A5 constructed from sample accession ERS1806693 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TCGAAGTG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#33.cram cram 1038077400.0 6920516.0 SC RUN 22829 8#33 0:75 1:75 A:270310565;C:245873612;G:245834117;T:274135301;N:1923805 75 75     270310565 245873612 245834117 274135301 1923805 ERX3468762 ERS1806693 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.9563 0.96046 0.13363 0.13125 0.67858 0.68095 0.49926 0.4941 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7914 7914 ERR3446762 ERX3468761 ERS1806695 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 A1 SAMEA104147677 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147677|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:39901d10 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39901d10 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934977                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#32 DN488439N:H4 Illumina sequencing of library DN488439N:H4 constructed from sample accession ERS1806695 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TTCCATTG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#32.cram cram 986612850.0 6577419.0 SC RUN 22829 8#32 0:75 1:75 A:259827485;C:230648413;G:231077889;T:263216608;N:1842455 75 75     259827485 230648413 231077889 263216608 1842455 ERX3468761 ERS1806695 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95392 0.95801 0.15749 0.15741 0.68633 0.68941 0.51453 0.5162 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7915 7915 ERR3446761 ERX3468760 ERS1806691 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 B1 SAMEA104147673 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147673|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:398547a0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:398547a0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934976                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#31 DN488439N:G4 Illumina sequencing of library DN488439N:G4 constructed from sample accession ERS1806691 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TAGTCTTG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#31.cram cram 1031442450.0 6876283.0 SC RUN 22829 8#31 0:75 1:75 A:274203878;C:238375461;G:238376358;T:278589476;N:1897277 75 75     274203878 238375461 238376358 278589476 1897277 ERX3468760 ERS1806691 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95118 0.95551 0.16324 0.16064 0.68615 0.68925 0.51221 0.50738 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7916 7916 ERR3446760 ERX3468759 ERS1806692 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 B8 SAMEA104147674 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147674|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:397a9940 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:397a9940 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934975                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#30 DN488439N:F4 Illumina sequencing of library DN488439N:F4 constructed from sample accession ERS1806692 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TGTGGTTG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#30.cram cram 841629750.0 5610865.0 SC RUN 22829 8#30 0:75 1:75 A:224237300;C:194199747;G:193893668;T:227725985;N:1573050 75 75     224237300 194199747 193893668 227725985 1573050 ERX3468759 ERS1806692 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95236 0.95666 0.15496 0.1528 0.68049 0.68406 0.50292 0.50201 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7917 7917 ERR3446759 ERX3468758 ERS1806690 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 C3 SAMEA104147672 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147672|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:396fc3d0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:396fc3d0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934974                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#29 DN488439N:E4 Illumina sequencing of library DN488439N:E4 constructed from sample accession ERS1806690 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TCCTCAAT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#29.cram cram 1003675800.0 6691172.0 SC RUN 22829 8#29 0:75 1:75 A:267034518;C:232079842;G:231287862;T:271430075;N:1843503 75 75     267034518 232079842 231287862 271430075 1843503 ERX3468758 ERS1806690 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95315 0.9573 0.15329 0.151 0.6869 0.68911 0.49176 0.49755 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7918 7918 ERR3446758 ERX3468757 ERS1806689 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 A2 SAMEA104147671 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147671|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:3962a470 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3962a470 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934973                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#28 DN488439N:D4 Illumina sequencing of library DN488439N:D4 constructed from sample accession ERS1806689 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TACAGGAT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#28.cram cram 877026750.0 5846845.0 SC RUN 22829 8#28 0:75 1:75 A:234056953;C:201909571;G:201550258;T:237878368;N:1631600 75 75     234056953 201909571 201550258 237878368 1631600 ERX3468757 ERS1806689 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95174 0.95506 0.16448 0.1594 0.68696 0.68956 0.51105 0.51529 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7919 7919 ERR3446757 ERX3468756 ERS1806688 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 B7 SAMEA104147670 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147670|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:3957cf00 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3957cf00 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934972                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#27 DN488439N:C4 Illumina sequencing of library DN488439N:C4 constructed from sample accession ERS1806688 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TAGTGACT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#27.cram cram 976188150.0 6507921.0 SC RUN 22829 8#27 0:75 1:75 A:258533450;C:226872670;G:226382560;T:262604964;N:1794506 75 75     258533450 226872670 226382560 262604964 1794506 ERX3468756 ERS1806688 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95189 0.95679 0.13942 0.13618 0.68274 0.68505 0.50235 0.50513 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7920 7920 ERR3446756 ERX3468755 ERS1806687 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 B2 SAMEA104147669 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147669|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:394a8890 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:394a8890 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934971                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#26 DN488439N:B4 Illumina sequencing of library DN488439N:B4 constructed from sample accession ERS1806687 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TTCCTGCT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#26.cram cram 893242800.0 5954952.0 SC RUN 22829 8#26 0:75 1:75 A:233780534;C:210342200;G:210386139;T:237085352;N:1648575 75 75     233780534 210342200 210386139 237085352 1648575 ERX3468755 ERS1806687 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.9547 0.95931 0.14551 0.14251 0.68605 0.6871 0.51109 0.51231 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7921 7921 ERR3446755 ERX3468754 ERS1806686 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 D6 SAMEA104147668 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147668|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:29Z|INSDC status:public|Submitter Id:393fb320 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:393fb320 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934970                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#25 DN488439N:A4 Illumina sequencing of library DN488439N:A4 constructed from sample accession ERS1806686 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TGCGATCT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#25.cram cram 990960750.0 6606405.0 SC RUN 22829 8#25 0:75 1:75 A:256751586;C:236231048;G:236105966;T:260051730;N:1820420 75 75     256751586 236231048 236105966 260051730 1820420 ERX3468754 ERS1806686 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95946 0.96347 0.13307 0.13209 0.68217 0.68505 0.4931 0.50013 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7922 7922 ERR3446754 ERX3468753 ERS1806685 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 E12 SAMEA104147667 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147667|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:29Z|INSDC status:public|Submitter Id:3931f780 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3931f780 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934969                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#24 DN488439N:H3 Illumina sequencing of library DN488439N:H3 constructed from sample accession ERS1806685 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TTGACTCT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#24.cram cram 964485000.0 6429900.0 SC RUN 22829 8#24 0:75 1:75 A:251451665;C:228331952;G:228439906;T:254469084;N:1792393 75 75     251451665 228331952 228439906 254469084 1792393 ERX3468753 ERS1806685 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.9564 0.96106 0.12973 0.12899 0.67876 0.68254 0.49322 0.4891 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7923 7923 ERR3446753 ERX3468752 ERS1806684 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 D4 SAMEA104147666 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147666|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:29Z|INSDC status:public|Submitter Id:39272210 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39272210 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934968                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#23 DN488439N:G3 Illumina sequencing of library DN488439N:G3 constructed from sample accession ERS1806684 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TGCATAGT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#23.cram cram 964272000.0 6428480.0 SC RUN 22829 8#23 0:75 1:75 A:251105580;C:228453524;G:228253397;T:254687699;N:1771800 75 75     251105580 228453524 228253397 254687699 1771800 ERX3468752 ERS1806684 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95716 0.96163 0.14819 0.14629 0.69016 0.69378 0.50746 0.51427 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7924 7924 ERR3446752 ERX3468751 ERS1806683 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 A3 SAMEA104147665 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147665|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:29Z|INSDC status:public|Submitter Id:391c4ca0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:391c4ca0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934967                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#22 DN488439N:F3 Illumina sequencing of library DN488439N:F3 constructed from sample accession ERS1806683 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TGATACGT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#22.cram cram 799230000.0 5328200.0 SC RUN 22829 8#22 0:75 1:75 A:212348969;C:184890796;G:184847246;T:215676416;N:1466573 75 75     212348969 184890796 184847246 215676416 1466573 ERX3468751 ERS1806683 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95436 0.95813 0.16036 0.1592 0.68759 0.69027 0.51144 0.50841 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7925 7925 ERR3446751 ERX3468750 ERS1806681 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 B6 SAMEA104147663 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147663|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:29Z|INSDC status:public|Submitter Id:3910b3e0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3910b3e0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934966                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#21 DN488439N:E3 Illumina sequencing of library DN488439N:E3 constructed from sample accession ERS1806681 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TCGAGCGT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#21.cram cram 923983200.0 6159888.0 SC RUN 22829 8#21 0:75 1:75 A:243217021;C:216142090;G:216007590;T:246916174;N:1700325 75 75     243217021 216142090 216007590 246916174 1700325 ERX3468750 ERS1806681 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95874 0.96248 0.14485 0.14306 0.69633 0.69877 0.5064 0.50544 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7926 7926 ERR3446750 ERX3468749 ERS1806682 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 B10 SAMEA104147664 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147664|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:29Z|INSDC status:public|Submitter Id:3905b760 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3905b760 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934965                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#20 DN488439N:D3 Illumina sequencing of library DN488439N:D3 constructed from sample accession ERS1806682 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TTGGAGGT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#20.cram cram 896749650.0 5978331.0 SC RUN 22829 8#20 0:75 1:75 A:236504641;C:209373052;G:209286381;T:239943497;N:1642079 75 75     236504641 209373052 209286381 239943497 1642079 ERX3468749 ERS1806682 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95456 0.9591 0.14445 0.14205 0.68544 0.68809 0.50085 0.50894 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7927 7927 ERR3446749 ERX3468748 ERS1806680 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 C7 SAMEA104147662 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147662|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:29Z|INSDC status:public|Submitter Id:38fae1f0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38fae1f0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934964                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#19 DN488439N:C3 Illumina sequencing of library DN488439N:C3 constructed from sample accession ERS1806680 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TCTGCTGT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#19.cram cram 933815700.0 6225438.0 SC RUN 22829 8#19 0:75 1:75 A:244718120;C:219569356;G:219612527;T:248215417;N:1700280 75 75     244718120 219569356 219612527 248215417 1700280 ERX3468748 ERS1806680 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95407 0.95781 0.14211 0.14014 0.68142 0.6845 0.5066 0.5032 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7928 7928 ERR3446748 ERX3468747 ERS1806678 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 A11 SAMEA104147660 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147660|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:28Z|INSDC status:public|Submitter Id:38f00c80 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38f00c80 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934963                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#18 DN488439N:B3 Illumina sequencing of library DN488439N:B3 constructed from sample accession ERS1806678 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TTCTGTGT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#18.cram cram 905329500.0 6035530.0 SC RUN 22829 8#18 0:75 1:75 A:240021393;C:210015428;G:210218903;T:243401797;N:1671979 75 75     240021393 210015428 210218903 243401797 1671979 ERX3468747 ERS1806678 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95212 0.95525 0.15692 0.15381 0.68254 0.68525 0.52037 0.5208 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7929 7929 ERR3446747 ERX3468746 ERS1806679 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 E3 SAMEA104147661 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147661|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:28Z|INSDC status:public|Submitter Id:38e51000 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38e51000 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934962                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#17 DN488439N:A3 Illumina sequencing of library DN488439N:A3 constructed from sample accession ERS1806679 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TGTACCTT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#17.cram cram 947665500.0 6317770.0 SC RUN 22829 8#17 0:75 1:75 A:246559305;C:224934978;G:224812411;T:249601963;N:1756843 75 75     246559305 224934978 224812411 249601963 1756843 ERX3468746 ERS1806679 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95666 0.96095 0.14463 0.14314 0.68757 0.68885 0.51144 0.51225 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7930 7930 ERR3446746 ERX3468745 ERS1806677 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 B4 SAMEA104147659 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147659|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:28Z|INSDC status:public|Submitter Id:38da3a90 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38da3a90 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934961                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#16 DN488439N:H2 Illumina sequencing of library DN488439N:H2 constructed from sample accession ERS1806677 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TCCGTCTT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#16.cram cram 1017363750.0 6782425.0 SC RUN 22829 8#16 0:75 1:75 A:265624052;C:240509411;G:240546256;T:268829904;N:1854127 75 75     265624052 240509411 240546256 268829904 1854127 ERX3468745 ERS1806677 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95466 0.95911 0.14109 0.13929 0.68199 0.68262 0.49544 0.4999 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7931 7931 ERR3446745 ERX3468744 ERS1806676 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 D3 SAMEA104147658 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147658|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:28Z|INSDC status:public|Submitter Id:38c8d570 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38c8d570 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934960                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#15 DN488439N:G2 Illumina sequencing of library DN488439N:G2 constructed from sample accession ERS1806676 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TAAGCGTT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#15.cram cram 1000345500.0 6668970.0 SC RUN 22829 8#15 0:75 1:75 A:258884239;C:238639192;G:238825356;T:262142988;N:1853725 75 75     258884239 238639192 238825356 262142988 1853725 ERX3468744 ERS1806676 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95861 0.96266 0.13649 0.13563 0.68755 0.69098 0.49977 0.50834 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7932 7932 ERR3446744 ERX3468743 ERS1806675 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 D7 SAMEA104147657 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147657|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:28Z|INSDC status:public|Submitter Id:38be0000 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38be0000 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934959                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#14 DN488439N:F2 Illumina sequencing of library DN488439N:F2 constructed from sample accession ERS1806675 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TCTCGGTT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#14.cram cram 831508200.0 5543388.0 SC RUN 22829 8#14 0:75 1:75 A:216944404;C:196565581;G:196615479;T:219853985;N:1528751 75 75     216944404 196565581 196615479 219853985 1528751 ERX3468743 ERS1806675 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95565 0.95932 0.13261 0.13138 0.67724 0.67971 0.49732 0.50908 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7933 7933 ERR3446743 ERX3468742 ERS1806674 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 C6 SAMEA104147656 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147656|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:28Z|INSDC status:public|Submitter Id:38b39fc0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38b39fc0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934958                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#13 DN488439N:E2 Illumina sequencing of library DN488439N:E2 constructed from sample accession ERS1806674 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TGGTTGTT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#13.cram cram 880251450.0 5868343.0 SC RUN 22829 8#13 0:75 1:75 A:230018306;C:207962954;G:207702793;T:232909633;N:1657764 75 75     230018306 207962954 207702793 232909633 1657764 ERX3468742 ERS1806674 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95442 0.95837 0.12979 0.12922 0.6762 0.68081 0.49384 0.49413 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7934 7934 ERR3446742 ERX3468741 ERS1806673 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 C9 SAMEA104147655 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147655|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:28Z|INSDC status:public|Submitter Id:38aa29e0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38aa29e0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934957                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#12 DN488439N:D2 Illumina sequencing of library DN488439N:D2 constructed from sample accession ERS1806673 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence CTTGTACT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#12.cram cram 885733500.0 5904890.0 SC RUN 22829 8#12 0:75 1:75 A:231281663;C:209310630;G:209302780;T:234229805;N:1608622 75 75     231281663 209310630 209302780 234229805 1608622 ERX3468741 ERS1806673 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95605 0.96017 0.13822 0.13754 0.68069 0.68385 0.50267 0.5053 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7935 7935 ERR3446741 ERX3468740 ERS1806672 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 B12 SAMEA104147654 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147654|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:28Z|INSDC status:public|Submitter Id:38a03ed0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38a03ed0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934956                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#11 DN488439N:C2 Illumina sequencing of library DN488439N:C2 constructed from sample accession ERS1806672 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence GGCTACAG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#11.cram cram 836620350.0 5577469.0 SC RUN 22829 8#11 0:75 1:75 A:219115747;C:196807550;G:197091855;T:222058678;N:1546520 75 75     219115747 196807550 197091855 222058678 1546520 ERX3468740 ERS1806672 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95466 0.95919 0.15021 0.14856 0.69043 0.69244 0.50929 0.51567 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7936 7936 ERR3446740 ERX3468739 ERS1806670 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 E2 SAMEA104147652 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147652|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:27Z|INSDC status:public|Submitter Id:38908760 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38908760 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934955                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#10 DN488439N:B2 Illumina sequencing of library DN488439N:B2 constructed from sample accession ERS1806670 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TAGCTTGT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#10.cram cram 911744850.0 6078299.0 SC RUN 22829 8#10 0:75 1:75 A:237470738;C:216053868;G:216099189;T:240450404;N:1670651 75 75     237470738 216053868 216099189 240450404 1670651 ERX3468739 ERS1806670 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95716 0.96092 0.14455 0.14187 0.68686 0.68954 0.50635 0.50911 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7937 7937 ERR3446739 ERX3468738 ERS1806671 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 C12 SAMEA104147653 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147653|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:27Z|INSDC status:public|Submitter Id:3886c360 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3886c360 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934954                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#9 DN488439N:A2 Illumina sequencing of library DN488439N:A2 constructed from sample accession ERS1806671 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence GATCAGCG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#9.cram cram 928894050.0 6192627.0 SC RUN 22829 8#9 0:75 1:75 A:243727946;C:218420567;G:218359552;T:246701233;N:1684752 75 75     243727946 218420567 218359552 246701233 1684752 ERX3468738 ERS1806671 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.9532 0.95745 0.14809 0.14652 0.68627 0.68911 0.5112 0.51053 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7938 7938 ERR3446738 ERX3468737 ERS1806669 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 B5 SAMEA104147651 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147651|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:27Z|INSDC status:public|Submitter Id:387c1500 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:387c1500 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934953                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#8 DN488439N:H1 Illumina sequencing of library DN488439N:H1 constructed from sample accession ERS1806669 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence ACTTGATG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#8.cram cram 930119400.0 6200796.0 SC RUN 22829 8#8 0:75 1:75 A:242979598;C:220045143;G:219448143;T:245941628;N:1704888 75 75     242979598 220045143 219448143 245941628 1704888 ERX3468737 ERS1806669 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95653 0.95946 0.14247 0.14149 0.6842 0.68738 0.4957 0.49737 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7939 7939 ERR3446737 ERX3468736 ERS1806667 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 D2 SAMEA104147649 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147649|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:27Z|INSDC status:public|Submitter Id:38729f20 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38729f20 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934952                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#7 DN488439N:G1 Illumina sequencing of library DN488439N:G1 constructed from sample accession ERS1806667 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence CAGATCTG. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#7.cram cram 992301900.0 6615346.0 SC RUN 22829 8#7 0:75 1:75 A:259898582;C:233807624;G:233974368;T:262804375;N:1816951 75 75     259898582 233807624 233974368 262804375 1816951 ERX3468736 ERS1806667 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95492 0.95925 0.14 0.13935 0.68112 0.68312 0.50181 0.49932 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7940 7940 ERR3446736 ERX3468735 ERS1806668 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 F2 SAMEA104147650 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147650|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:27Z|INSDC status:public|Submitter Id:385e05b0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:385e05b0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934951                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#6 DN488439N:F1 Illumina sequencing of library DN488439N:F1 constructed from sample accession ERS1806668 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence GCCAATGT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#6.cram cram 875586600.0 5837244.0 SC RUN 22829 8#6 0:75 1:75 A:231423685;C:204253857;G:204201395;T:234093029;N:1614634 75 75     231423685 204253857 204201395 234093029 1614634 ERX3468735 ERS1806668 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95428 0.95811 0.15334 0.15296 0.67905 0.68256 0.50447 0.50735 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7941 7941 ERR3446735 ERX3468734 ERS1806666 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 A4 SAMEA104147648 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147648|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:27Z|INSDC status:public|Submitter Id:384833c0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:384833c0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934950                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#5 DN488439N:E1 Illumina sequencing of library DN488439N:E1 constructed from sample accession ERS1806666 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence ACAGTGGT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#5.cram cram 835599450.0 5570663.0 SC RUN 22829 8#5 0:75 1:75 A:221022844;C:194609457;G:194728372;T:223667754;N:1571023 75 75     221022844 194609457 194728372 223667754 1571023 ERX3468734 ERS1806666 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95389 0.95704 0.16434 0.16289 0.68363 0.68669 0.50299 0.51388 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7942 7942 ERR3446734 ERX3468733 ERS1806664 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 F1 SAMEA104147646 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147646|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:26Z|INSDC status:public|Submitter Id:3832aff0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3832aff0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934949                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#4 DN488439N:D1 Illumina sequencing of library DN488439N:D1 constructed from sample accession ERS1806664 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TGACCACT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#4.cram cram 891655350.0 5944369.0 SC RUN 22829 8#4 0:75 1:75 A:236505554;C:207018655;G:207193827;T:239299452;N:1637862 75 75     236505554 207018655 207193827 239299452 1637862 ERX3468733 ERS1806664 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95251 0.95547 0.16653 0.16502 0.68822 0.68984 0.51935 0.51421 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7943 7943 ERR3446733 ERX3468732 ERS1806665 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 C2 SAMEA104147647 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147647|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:26Z|INSDC status:public|Submitter Id:38138f30 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38138f30 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934948                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#3 DN488439N:C1 Illumina sequencing of library DN488439N:C1 constructed from sample accession ERS1806665 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence TTAGGCAT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#3.cram cram 888434250.0 5922895.0 SC RUN 22829 8#3 0:75 1:75 A:233268153;C:208683895;G:208766742;T:236094656;N:1620804 75 75     233268153 208683895 208766742 236094656 1620804 ERX3468732 ERS1806665 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95631 0.96066 0.14611 0.14537 0.68422 0.6854 0.50209 0.50377 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7944 7944 ERR3446732 ERX3468731 ERS1806663 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 B3 SAMEA104147645 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147645|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:26Z|INSDC status:public|Submitter Id:37fdbd40 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:37fdbd40 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934947                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#2 DN488439N:B1 Illumina sequencing of library DN488439N:B1 constructed from sample accession ERS1806663 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence CGATGTTT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#2.cram cram 883215600.0 5888104.0 SC RUN 22829 8#2 0:75 1:75 A:231296783;C:208055844;G:208135446;T:234080007;N:1647520 75 75     231296783 208055844 208135446 234080007 1647520 ERX3468731 ERS1806663 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95417 0.95779 0.14224 0.14158 0.67945 0.68178 0.49376 0.49496 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
7945 7945 ERR3446731 ERX3468730 ERS1806662 ERP023267 PRJEB21045 RNASeq of zebrafish metabolic mutants RNASeq_of_zebrafish_metabolic_mutants-sc-4765 Transcriptome Analysis RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis. ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683     zmp ph279 E4 SAMEA104147644 Wellcome Sanger Institute ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147644|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:26Z|INSDC status:public|Submitter Id:37e37e80 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:37e37e80 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934946                 Illumina HiSeq 2500 paired end sequencing SC EXP 22829 8#1 DN488439N:A1 Illumina sequencing of library DN488439N:A1 constructed from sample accession ERS1806662 for study accession ERP023267. This is part of an Illumina multiplexed sequencing run 22829 8. This submission includes reads tagged with the sequence ATCACGTT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   ERP023267 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22 22829_8#1.cram cram 832221450.0 5548143.0 SC RUN 22829 8#1 0:75 1:75 A:218233303;C:195802305;G:195652594;T:221003769;N:1529479 75 75     218233303 195802305 195652594 221003769 1529479 ERX3468730 ERS1806662 ERA2044656 European Nucleotide Archive Wellcome Sanger Institute 2 0.95539 0.95958 0.13422 0.13299 0.68631 0.68828 0.49563 0.49505 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United Kingdom 2017-05-25 Larval Larval Whole Organism All anatomical structures
9699 9699 ERR3301006 ERX3327073 ERS3389661 ERP115040 PRJEB32363 RNA seq of zebrafish sa12692 mutants against WT controls E-MTAB-7920 Transcriptome Analysis Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30   Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… WT embryo rep 3 SAMEA5585437 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585437|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT embryo rep 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:normal|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:WT embryo rep 3|scientific name:Danio rerio|strain:AB                 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls E MTAB 7920:WT embryo rep 3 p WT embryo rep 3 p RNA seq of zebrafish sa12692 mutants against WT controls Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP115040 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo3_2.fq.gz fastq fastq 7308473280.0 45677958.0 E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTembryo3 0:80 1:80 A:1898812783;C:1731426486;G:1757309247;T:1920031807;N:892957 80 80     1898812783 1731426486 1757309247 1920031807 892957 ERX3327073 ERS3389661 ERA1880314 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive 2 0.94288 0.95671 0.07985 0.08023 0.67915 0.67815 0.47781 0.48461 80 80 B B biological fallback assumption illumina nextseq 3prime poly_a trueseq bulk bulk bulk   Ireland 2019-04-30 Larval Larval Whole Organism All anatomical structures
9700 9700 ERR3301005 ERX3327072 ERS3389660 ERP115040 PRJEB32363 RNA seq of zebrafish sa12692 mutants against WT controls E-MTAB-7920 Transcriptome Analysis Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30   Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… WT embryo rep 2 SAMEA5585436 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585436|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT embryo rep 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:normal|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:WT embryo rep 2|scientific name:Danio rerio|strain:AB                 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls E MTAB 7920:WT embryo rep 2 p WT embryo rep 2 p RNA seq of zebrafish sa12692 mutants against WT controls Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP115040 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo2_2.fq.gz fastq fastq 7424396000.0 46402475.0 E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTembryo2 0:80 1:80 A:1940921070;C:1754354124;G:1768688429;T:1959515088;N:917289 80 80     1940921070 1754354124 1768688429 1959515088 917289 ERX3327072 ERS3389660 ERA1880314 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive 2 0.94222 0.95663 0.0909 0.09022 0.67929 0.67606 0.48763 0.48719 80 80 B B biological fallback assumption illumina nextseq 3prime poly_a trueseq bulk bulk bulk   Ireland 2019-04-30 Larval Larval Whole Organism All anatomical structures
9701 9701 ERR3301004 ERX3327071 ERS3389659 ERP115040 PRJEB32363 RNA seq of zebrafish sa12692 mutants against WT controls E-MTAB-7920 Transcriptome Analysis Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30   Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… WT embryo rep 1 SAMEA5585435 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585435|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT embryo rep 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:normal|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:WT embryo rep 1|scientific name:Danio rerio|strain:AB                 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls E MTAB 7920:WT embryo rep 1 p WT embryo rep 1 p RNA seq of zebrafish sa12692 mutants against WT controls Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP115040 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo1_2.fq.gz fastq fastq 7300913760.0 45630711.0 E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTembryo1 0:80 1:80 A:1931507380;C:1703881934;G:1712942848;T:1951676424;N:905174 80 80     1931507380 1703881934 1712942848 1951676424 905174 ERX3327071 ERS3389659 ERA1880314 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive 2 0.93831 0.95401 0.09471 0.09526 0.67576 0.67403 0.48092 0.48297 80 80 B B biological fallback assumption illumina nextseq 3prime poly_a trueseq bulk bulk bulk   Ireland 2019-04-30 Larval Larval Whole Organism All anatomical structures
9705 9705 ERR3301000 ERX3327067 ERS3389655 ERP115040 PRJEB32363 RNA seq of zebrafish sa12692 mutants against WT controls E-MTAB-7920 Transcriptome Analysis Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30   Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… Mutant embryo rep 3 SAMEA5585431 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585431|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant embryo rep 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:Naxos disease|genotype:sa12692 mutant|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:Mutant embryo rep 3|scientific name:Danio rerio|strain:sa12692 mutant                 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls E MTAB 7920:Mutant embryo rep 3 p Mutant embryo rep 3 p RNA seq of zebrafish sa12692 mutants against WT controls Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP115040 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo3_2.fq.gz fastq fastq 6323854560.0 39524091.0 E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantembryo3 0:80 1:80 A:1662088892;C:1473777430;G:1500364334;T:1686853051;N:770853 80 80     1662088892 1473777430 1500364334 1686853051 770853 ERX3327067 ERS3389655 ERA1880314 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive 2 0.93548 0.95404 0.09034 0.09103 0.67584 0.67592 0.47892 0.48193 80 80 B B biological fallback assumption illumina nextseq 3prime poly_a trueseq bulk bulk bulk   Ireland 2019-04-30 Larval Larval Whole Organism All anatomical structures
9706 9706 ERR3300999 ERX3327066 ERS3389654 ERP115040 PRJEB32363 RNA seq of zebrafish sa12692 mutants against WT controls E-MTAB-7920 Transcriptome Analysis Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30   Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… Mutant embryo rep 2 SAMEA5585430 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585430|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant embryo rep 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:Naxos disease|genotype:sa12692 mutant|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:Mutant embryo rep 2|scientific name:Danio rerio|strain:sa12692 mutant                 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls E MTAB 7920:Mutant embryo rep 2 p Mutant embryo rep 2 p RNA seq of zebrafish sa12692 mutants against WT controls Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP115040 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo2_2.fq.gz fastq fastq 6564227680.0 41026423.0 E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantembryo2 0:80 1:80 A:1702331829;C:1557343680;G:1583770440;T:1719974488;N:807243 80 80     1702331829 1557343680 1583770440 1719974488 807243 ERX3327066 ERS3389654 ERA1880314 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive 2 0.94141 0.95836 0.07518 0.07501 0.67982 0.67803 0.47895 0.47763 80 80 B B biological fallback assumption illumina nextseq 3prime poly_a trueseq bulk bulk bulk   Ireland 2019-04-30 Larval Larval Whole Organism All anatomical structures
9707 9707 ERR3300998 ERX3327065 ERS3389653 ERP115040 PRJEB32363 RNA seq of zebrafish sa12692 mutants against WT controls E-MTAB-7920 Transcriptome Analysis Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30   Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… Mutant embryo rep 1 SAMEA5585429 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585429|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant embryo rep 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:Naxos disease|genotype:sa12692 mutant|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:Mutant embryo rep 1|scientific name:Danio rerio|strain:sa12692 mutant                 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls E MTAB 7920:Mutant embryo rep 1 p Mutant embryo rep 1 p RNA seq of zebrafish sa12692 mutants against WT controls Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP115040 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo1_2.fq.gz fastq fastq 6991429280.0 43696433.0 E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantembryo1 0:80 1:80 A:1852543850;C:1630880197;G:1635963943;T:1871173669;N:867621 80 80     1852543850 1630880197 1635963943 1871173669 867621 ERX3327065 ERS3389653 ERA1880314 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive 2 0.93819 0.95201 0.10106 0.10107 0.67541 0.67523 0.4792 0.48253 80 80 B B biological fallback assumption illumina nextseq 3prime poly_a trueseq bulk bulk bulk   Ireland 2019-04-30 Larval Larval Whole Organism All anatomical structures
9816 9816 ERR3957806 ERX3965610 ERS4355893 ERP120207 PRJEB36940 RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E-MTAB-8824 Transcriptome Analysis Cutis laxa CL syndromes are a heterogenous group of connective tissue disorders that share a loose redundant skin as a common clinical feature. The systemic features vary among the different subtypes. CL is caused by mutations in genes encoding for components of the extracellular matrix FBLN4 FBLN5 LTBP4 and ELN encoding for elastin modifying enzymes ATP7A or encoding for components that influence cellular trafficking and metabolism ATP6V1E1 ATP6V1A ATP6V0A2 ALDH18A1 RIN2 GORAB PYCR1 and SLC2A10. ATP6V1E1–related CL cause loose redundant skin folds variable mental disability typical facial characteristics lipodystrophy hypotonia and cardiopulmonary involvement including pneumothorax hypertrophic cardiomyopathy and aortic root dilatation. The intent of this study is to investigate which genes are up or downregulated in atp6v1e1b deficient zebrafish larvae compared to wild type controls. Via transcriptome analysis we want to study the pathogenic mechanism of ATP6V1E1 induced CL syndrome. We use a zebrafish line with viral insertion in the five primeUTR of atp6v1e1b disrupting transcription atp6v1e1bhi577aTg/+ from the Zebrafish International Research Center ZIRC and we use a line harboring a two base pair insertion followed by a three base pair deletion in exon 5 of atp6v1e1b c.334insGG; c.337 340delCGG predicted to result in p.R111WfsX2 atp6v1e1bcmg78/+ which we created ourselves by CRISPR Cas9 mutagenesis. Overview of the experimental work flow: Sample collection: pool of 10 zebrafish larvae of 3 dpf/genotype in RNA later RNA extraction: TRIzol® Reagent RNeasy mini kit Qiagen according to manufacturer's instructions RNA integrity: 2100 Bioanalyzer Agilent Sequencing library: TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina Sequencing: HiSeq 3000 sequencer Illumina paired end 150 bp sequencing facility of the Center of Medical Genetics Ghent alignement to zebrafish GRCz10 reference g… ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26   Protocols: Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. atp6v1e1b hi577aTg/hi577aTg 3 SAMEA6591599 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University ENA FIRST PUBLIC:2020 08 03T04:04:15Z|ENA LAST UPDATE:2020 02 26T13:29:54Z|External Id:SAMEA6591599|INSDC center name:Center for Medical Genetics Ghent Ghent University Hospital Ghent Belgium Department of biomolecular medicine Ghent University|INSDC first public:2020 08 03T04:04:15Z|INSDC last update:2020 02 26T13:29:54Z|INSDC status:public|Submitter Id:E MTAB 8824:atp6v1e1b hi577aTg/hi577aTg 3|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|disease:Autosomal recessive cutis laxa type 2A|disease staging:before the gross morphological phenotype becomes apparent|genetic modification:insertion|genotype:atp6v1e1b hi577aTg/hi577aTg|individual:pool of 10 larvae|organism part:whole organism|phenotype:atp6v1e1b deletion|replicate:biological replicate|sample name:E MTAB 8824:atp6v1e1b hi577aTg/hi577aTg 3|scientific name:Danio rerio|sex:male|strain:AB                 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E MTAB 8824:atp6v1e1b hi577aTg/hi577aTg 3 p atp6v1e1b hi577aTg/hi577aTg 3 p RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. Experimental Factor: genotype:atp6v1e1b hi577aTg/hi577aTg|Experimental Factor: disease:Autosomal recessive cutis laxa type 2A RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 3000   ERP120207 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26 atp6v1e1b_hi577aTghi577aTg_3_R1.fastq.gz atp6v1e1b_hi577aTghi577aTg_3_R2.fastq.gz fastq fastq 9237478586.0 31595868.0 E MTAB 8824:atp6v1e1b hi577aTghi577aTg 3 R 0:146.21 1:146.15 A:2400784505;C:2208559586;G:2203025457;T:2422549514;N:2559524 146 146     2400784505 2208559586 2203025457 2422549514 2559524 ERX3965610 ERS4355893 ERA2393549 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive 2 0.95009 0.95029 0.06098 0.05862 0.66736 0.67614 0.46036 0.46726 140 140 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2020-02-26 Larval Larval Whole Organism All anatomical structures
9817 9817 ERR3957805 ERX3965609 ERS4355892 ERP120207 PRJEB36940 RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E-MTAB-8824 Transcriptome Analysis Cutis laxa CL syndromes are a heterogenous group of connective tissue disorders that share a loose redundant skin as a common clinical feature. The systemic features vary among the different subtypes. CL is caused by mutations in genes encoding for components of the extracellular matrix FBLN4 FBLN5 LTBP4 and ELN encoding for elastin modifying enzymes ATP7A or encoding for components that influence cellular trafficking and metabolism ATP6V1E1 ATP6V1A ATP6V0A2 ALDH18A1 RIN2 GORAB PYCR1 and SLC2A10. ATP6V1E1–related CL cause loose redundant skin folds variable mental disability typical facial characteristics lipodystrophy hypotonia and cardiopulmonary involvement including pneumothorax hypertrophic cardiomyopathy and aortic root dilatation. The intent of this study is to investigate which genes are up or downregulated in atp6v1e1b deficient zebrafish larvae compared to wild type controls. Via transcriptome analysis we want to study the pathogenic mechanism of ATP6V1E1 induced CL syndrome. We use a zebrafish line with viral insertion in the five primeUTR of atp6v1e1b disrupting transcription atp6v1e1bhi577aTg/+ from the Zebrafish International Research Center ZIRC and we use a line harboring a two base pair insertion followed by a three base pair deletion in exon 5 of atp6v1e1b c.334insGG; c.337 340delCGG predicted to result in p.R111WfsX2 atp6v1e1bcmg78/+ which we created ourselves by CRISPR Cas9 mutagenesis. Overview of the experimental work flow: Sample collection: pool of 10 zebrafish larvae of 3 dpf/genotype in RNA later RNA extraction: TRIzol® Reagent RNeasy mini kit Qiagen according to manufacturer's instructions RNA integrity: 2100 Bioanalyzer Agilent Sequencing library: TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina Sequencing: HiSeq 3000 sequencer Illumina paired end 150 bp sequencing facility of the Center of Medical Genetics Ghent alignement to zebrafish GRCz10 reference g… ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26   Protocols: Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. atp6v1e1b hi577aTg/hi577aTg 2 SAMEA6591598 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University ENA FIRST PUBLIC:2020 08 03T04:04:15Z|ENA LAST UPDATE:2020 02 26T13:29:54Z|External Id:SAMEA6591598|INSDC center name:Center for Medical Genetics Ghent Ghent University Hospital Ghent Belgium Department of biomolecular medicine Ghent University|INSDC first public:2020 08 03T04:04:15Z|INSDC last update:2020 02 26T13:29:54Z|INSDC status:public|Submitter Id:E MTAB 8824:atp6v1e1b hi577aTg/hi577aTg 2|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|disease:Autosomal recessive cutis laxa type 2A|disease staging:before the gross morphological phenotype becomes apparent|genetic modification:insertion|genotype:atp6v1e1b hi577aTg/hi577aTg|individual:pool of 10 larvae|organism part:whole organism|phenotype:atp6v1e1b deletion|replicate:biological replicate|sample name:E MTAB 8824:atp6v1e1b hi577aTg/hi577aTg 2|scientific name:Danio rerio|sex:male|strain:AB                 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E MTAB 8824:atp6v1e1b hi577aTg/hi577aTg 2 p atp6v1e1b hi577aTg/hi577aTg 2 p RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. Experimental Factor: genotype:atp6v1e1b hi577aTg/hi577aTg|Experimental Factor: disease:Autosomal recessive cutis laxa type 2A RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 3000   ERP120207 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26 atp6v1e1b_hi577aTghi577aTg_2_R1.fastq.gz atp6v1e1b_hi577aTghi577aTg_2_R2.fastq.gz fastq fastq 12062097051.0 41147017.0 E MTAB 8824:atp6v1e1b hi577aTghi577aTg 2 R 0:146.61 1:146.54 A:3154735338;C:2867420665;G:2850251799;T:3187999165;N:1690084 146 146     3154735338 2867420665 2850251799 3187999165 1690084 ERX3965609 ERS4355892 ERA2393549 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive 2 0.94863 0.94866 0.0678 0.06563 0.66421 0.67188 0.46715 0.45279 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2020-02-26 Larval Larval Whole Organism All anatomical structures
9818 9818 ERR3957804 ERX3965608 ERS4355891 ERP120207 PRJEB36940 RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E-MTAB-8824 Transcriptome Analysis Cutis laxa CL syndromes are a heterogenous group of connective tissue disorders that share a loose redundant skin as a common clinical feature. The systemic features vary among the different subtypes. CL is caused by mutations in genes encoding for components of the extracellular matrix FBLN4 FBLN5 LTBP4 and ELN encoding for elastin modifying enzymes ATP7A or encoding for components that influence cellular trafficking and metabolism ATP6V1E1 ATP6V1A ATP6V0A2 ALDH18A1 RIN2 GORAB PYCR1 and SLC2A10. ATP6V1E1–related CL cause loose redundant skin folds variable mental disability typical facial characteristics lipodystrophy hypotonia and cardiopulmonary involvement including pneumothorax hypertrophic cardiomyopathy and aortic root dilatation. The intent of this study is to investigate which genes are up or downregulated in atp6v1e1b deficient zebrafish larvae compared to wild type controls. Via transcriptome analysis we want to study the pathogenic mechanism of ATP6V1E1 induced CL syndrome. We use a zebrafish line with viral insertion in the five primeUTR of atp6v1e1b disrupting transcription atp6v1e1bhi577aTg/+ from the Zebrafish International Research Center ZIRC and we use a line harboring a two base pair insertion followed by a three base pair deletion in exon 5 of atp6v1e1b c.334insGG; c.337 340delCGG predicted to result in p.R111WfsX2 atp6v1e1bcmg78/+ which we created ourselves by CRISPR Cas9 mutagenesis. Overview of the experimental work flow: Sample collection: pool of 10 zebrafish larvae of 3 dpf/genotype in RNA later RNA extraction: TRIzol® Reagent RNeasy mini kit Qiagen according to manufacturer's instructions RNA integrity: 2100 Bioanalyzer Agilent Sequencing library: TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina Sequencing: HiSeq 3000 sequencer Illumina paired end 150 bp sequencing facility of the Center of Medical Genetics Ghent alignement to zebrafish GRCz10 reference g… ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26   Protocols: Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. atp6v1e1b hi577aTg/hi577aTg 1 SAMEA6591597 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University ENA FIRST PUBLIC:2020 08 03T04:04:15Z|ENA LAST UPDATE:2020 02 26T13:29:54Z|External Id:SAMEA6591597|INSDC center name:Center for Medical Genetics Ghent Ghent University Hospital Ghent Belgium Department of biomolecular medicine Ghent University|INSDC first public:2020 08 03T04:04:15Z|INSDC last update:2020 02 26T13:29:54Z|INSDC status:public|Submitter Id:E MTAB 8824:atp6v1e1b hi577aTg/hi577aTg 1|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|disease:Autosomal recessive cutis laxa type 2A|disease staging:before the gross morphological phenotype becomes apparent|genetic modification:insertion|genotype:atp6v1e1b hi577aTg/hi577aTg|individual:pool of 10 larvae|organism part:whole organism|phenotype:atp6v1e1b deletion|replicate:biological replicate|sample name:E MTAB 8824:atp6v1e1b hi577aTg/hi577aTg 1|scientific name:Danio rerio|sex:male|strain:AB                 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E MTAB 8824:atp6v1e1b hi577aTg/hi577aTg 1 p atp6v1e1b hi577aTg/hi577aTg 1 p RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. Experimental Factor: genotype:atp6v1e1b hi577aTg/hi577aTg|Experimental Factor: disease:Autosomal recessive cutis laxa type 2A RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 3000   ERP120207 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26 atp6v1e1b_hi577aTghi577aTg_1_R1.fastq.gz atp6v1e1b_hi577aTghi577aTg_1_R2.fastq.gz fastq fastq 11019227010.0 37395805.0 E MTAB 8824:atp6v1e1b hi577aTghi577aTg 1 R 0:147.37 1:147.30 A:2899320822;C:2600085014;G:2589161285;T:2928994069;N:1665820 147 147     2899320822 2600085014 2589161285 2928994069 1665820 ERX3965608 ERS4355891 ERA2393549 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive 2 0.94632 0.94707 0.07358 0.07016 0.66543 0.67357 0.46855 0.47148 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2020-02-26 Larval Larval Whole Organism All anatomical structures
9819 9819 ERR3957803 ERX3965607 ERS4355890 ERP120207 PRJEB36940 RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E-MTAB-8824 Transcriptome Analysis Cutis laxa CL syndromes are a heterogenous group of connective tissue disorders that share a loose redundant skin as a common clinical feature. The systemic features vary among the different subtypes. CL is caused by mutations in genes encoding for components of the extracellular matrix FBLN4 FBLN5 LTBP4 and ELN encoding for elastin modifying enzymes ATP7A or encoding for components that influence cellular trafficking and metabolism ATP6V1E1 ATP6V1A ATP6V0A2 ALDH18A1 RIN2 GORAB PYCR1 and SLC2A10. ATP6V1E1–related CL cause loose redundant skin folds variable mental disability typical facial characteristics lipodystrophy hypotonia and cardiopulmonary involvement including pneumothorax hypertrophic cardiomyopathy and aortic root dilatation. The intent of this study is to investigate which genes are up or downregulated in atp6v1e1b deficient zebrafish larvae compared to wild type controls. Via transcriptome analysis we want to study the pathogenic mechanism of ATP6V1E1 induced CL syndrome. We use a zebrafish line with viral insertion in the five primeUTR of atp6v1e1b disrupting transcription atp6v1e1bhi577aTg/+ from the Zebrafish International Research Center ZIRC and we use a line harboring a two base pair insertion followed by a three base pair deletion in exon 5 of atp6v1e1b c.334insGG; c.337 340delCGG predicted to result in p.R111WfsX2 atp6v1e1bcmg78/+ which we created ourselves by CRISPR Cas9 mutagenesis. Overview of the experimental work flow: Sample collection: pool of 10 zebrafish larvae of 3 dpf/genotype in RNA later RNA extraction: TRIzol® Reagent RNeasy mini kit Qiagen according to manufacturer's instructions RNA integrity: 2100 Bioanalyzer Agilent Sequencing library: TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina Sequencing: HiSeq 3000 sequencer Illumina paired end 150 bp sequencing facility of the Center of Medical Genetics Ghent alignement to zebrafish GRCz10 reference g… ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26   Protocols: Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. atp6v1e1b cmg78/cmg78 3 SAMEA6591596 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University ENA FIRST PUBLIC:2020 08 03T04:04:15Z|ENA LAST UPDATE:2020 02 26T13:29:54Z|External Id:SAMEA6591596|INSDC center name:Center for Medical Genetics Ghent Ghent University Hospital Ghent Belgium Department of biomolecular medicine Ghent University|INSDC first public:2020 08 03T04:04:15Z|INSDC last update:2020 02 26T13:29:54Z|INSDC status:public|Submitter Id:E MTAB 8824:atp6v1e1b cmg78/cmg78 3|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|disease:Autosomal recessive cutis laxa type 2A|disease staging:before the gross morphological phenotype becomes apparent|genetic modification:gene knock out|genotype:atp6v1e1b cmg78/cmg78|individual:pool of 10 larvae|organism part:whole organism|phenotype:atp6v1e1b deletion|replicate:biological replicate|sample name:E MTAB 8824:atp6v1e1b cmg78/cmg78 3|scientific name:Danio rerio|sex:male|strain:AB                 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E MTAB 8824:atp6v1e1b cmg78/cmg78 3 p atp6v1e1b cmg78/cmg78 3 p RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. Experimental Factor: genotype:atp6v1e1b cmg78/cmg78|Experimental Factor: disease:Autosomal recessive cutis laxa type 2A RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 3000   ERP120207 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26 atp6v1e1b_cmg78cmg78_3_R1.fastq.gz atp6v1e1b_cmg78cmg78_3_R2.fastq.gz fastq fastq 11394931126.0 38868508.0 E MTAB 8824:atp6v1e1b cmg78cmg78 3 R 0:146.62 1:146.54 A:2997347418;C:2691952662;G:2671891078;T:3032072506;N:1667462 146 146     2997347418 2691952662 2671891078 3032072506 1667462 ERX3965607 ERS4355890 ERA2393549 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive 2 0.94663 0.94787 0.07048 0.0672 0.66444 0.67105 0.46855 0.46335 151 150 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2020-02-26 Larval Larval Whole Organism All anatomical structures
9820 9820 ERR3957802 ERX3965606 ERS4355889 ERP120207 PRJEB36940 RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E-MTAB-8824 Transcriptome Analysis Cutis laxa CL syndromes are a heterogenous group of connective tissue disorders that share a loose redundant skin as a common clinical feature. The systemic features vary among the different subtypes. CL is caused by mutations in genes encoding for components of the extracellular matrix FBLN4 FBLN5 LTBP4 and ELN encoding for elastin modifying enzymes ATP7A or encoding for components that influence cellular trafficking and metabolism ATP6V1E1 ATP6V1A ATP6V0A2 ALDH18A1 RIN2 GORAB PYCR1 and SLC2A10. ATP6V1E1–related CL cause loose redundant skin folds variable mental disability typical facial characteristics lipodystrophy hypotonia and cardiopulmonary involvement including pneumothorax hypertrophic cardiomyopathy and aortic root dilatation. The intent of this study is to investigate which genes are up or downregulated in atp6v1e1b deficient zebrafish larvae compared to wild type controls. Via transcriptome analysis we want to study the pathogenic mechanism of ATP6V1E1 induced CL syndrome. We use a zebrafish line with viral insertion in the five primeUTR of atp6v1e1b disrupting transcription atp6v1e1bhi577aTg/+ from the Zebrafish International Research Center ZIRC and we use a line harboring a two base pair insertion followed by a three base pair deletion in exon 5 of atp6v1e1b c.334insGG; c.337 340delCGG predicted to result in p.R111WfsX2 atp6v1e1bcmg78/+ which we created ourselves by CRISPR Cas9 mutagenesis. Overview of the experimental work flow: Sample collection: pool of 10 zebrafish larvae of 3 dpf/genotype in RNA later RNA extraction: TRIzol® Reagent RNeasy mini kit Qiagen according to manufacturer's instructions RNA integrity: 2100 Bioanalyzer Agilent Sequencing library: TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina Sequencing: HiSeq 3000 sequencer Illumina paired end 150 bp sequencing facility of the Center of Medical Genetics Ghent alignement to zebrafish GRCz10 reference g… ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26   Protocols: Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. atp6v1e1b cmg78/cmg78 2 SAMEA6591595 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University ENA FIRST PUBLIC:2020 08 03T04:04:15Z|ENA LAST UPDATE:2020 02 26T13:29:54Z|External Id:SAMEA6591595|INSDC center name:Center for Medical Genetics Ghent Ghent University Hospital Ghent Belgium Department of biomolecular medicine Ghent University|INSDC first public:2020 08 03T04:04:15Z|INSDC last update:2020 02 26T13:29:54Z|INSDC status:public|Submitter Id:E MTAB 8824:atp6v1e1b cmg78/cmg78 2|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|disease:Autosomal recessive cutis laxa type 2A|disease staging:before the gross morphological phenotype becomes apparent|genetic modification:gene knock out|genotype:atp6v1e1b cmg78/cmg78|individual:pool of 10 larvae|organism part:whole organism|phenotype:atp6v1e1b deletion|replicate:biological replicate|sample name:E MTAB 8824:atp6v1e1b cmg78/cmg78 2|scientific name:Danio rerio|sex:male|strain:AB                 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E MTAB 8824:atp6v1e1b cmg78/cmg78 2 p atp6v1e1b cmg78/cmg78 2 p RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. Experimental Factor: genotype:atp6v1e1b cmg78/cmg78|Experimental Factor: disease:Autosomal recessive cutis laxa type 2A RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 3000   ERP120207 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26 atp6v1e1b_cmg78cmg78_2_R1.fastq.gz atp6v1e1b_cmg78cmg78_2_R2.fastq.gz fastq fastq 9970017982.0 33968628.0 E MTAB 8824:atp6v1e1b cmg78cmg78 2 R 0:146.79 1:146.72 A:2605084972;C:2371579416;G:2361363755;T:2629380392;N:2609447 146 146     2605084972 2371579416 2361363755 2629380392 2609447 ERX3965606 ERS4355889 ERA2393549 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive 2 0.9492 0.94939 0.06589 0.06313 0.66576 0.67373 0.46451 0.45372 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2020-02-26 Larval Larval Whole Organism All anatomical structures
9821 9821 ERR3957801 ERX3965605 ERS4355888 ERP120207 PRJEB36940 RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E-MTAB-8824 Transcriptome Analysis Cutis laxa CL syndromes are a heterogenous group of connective tissue disorders that share a loose redundant skin as a common clinical feature. The systemic features vary among the different subtypes. CL is caused by mutations in genes encoding for components of the extracellular matrix FBLN4 FBLN5 LTBP4 and ELN encoding for elastin modifying enzymes ATP7A or encoding for components that influence cellular trafficking and metabolism ATP6V1E1 ATP6V1A ATP6V0A2 ALDH18A1 RIN2 GORAB PYCR1 and SLC2A10. ATP6V1E1–related CL cause loose redundant skin folds variable mental disability typical facial characteristics lipodystrophy hypotonia and cardiopulmonary involvement including pneumothorax hypertrophic cardiomyopathy and aortic root dilatation. The intent of this study is to investigate which genes are up or downregulated in atp6v1e1b deficient zebrafish larvae compared to wild type controls. Via transcriptome analysis we want to study the pathogenic mechanism of ATP6V1E1 induced CL syndrome. We use a zebrafish line with viral insertion in the five primeUTR of atp6v1e1b disrupting transcription atp6v1e1bhi577aTg/+ from the Zebrafish International Research Center ZIRC and we use a line harboring a two base pair insertion followed by a three base pair deletion in exon 5 of atp6v1e1b c.334insGG; c.337 340delCGG predicted to result in p.R111WfsX2 atp6v1e1bcmg78/+ which we created ourselves by CRISPR Cas9 mutagenesis. Overview of the experimental work flow: Sample collection: pool of 10 zebrafish larvae of 3 dpf/genotype in RNA later RNA extraction: TRIzol® Reagent RNeasy mini kit Qiagen according to manufacturer's instructions RNA integrity: 2100 Bioanalyzer Agilent Sequencing library: TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina Sequencing: HiSeq 3000 sequencer Illumina paired end 150 bp sequencing facility of the Center of Medical Genetics Ghent alignement to zebrafish GRCz10 reference g… ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26   Protocols: Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. atp6v1e1b cmg78/cmg78 1 SAMEA6591594 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University ENA FIRST PUBLIC:2020 08 03T04:04:15Z|ENA LAST UPDATE:2020 02 26T13:29:54Z|External Id:SAMEA6591594|INSDC center name:Center for Medical Genetics Ghent Ghent University Hospital Ghent Belgium Department of biomolecular medicine Ghent University|INSDC first public:2020 08 03T04:04:15Z|INSDC last update:2020 02 26T13:29:54Z|INSDC status:public|Submitter Id:E MTAB 8824:atp6v1e1b cmg78/cmg78 1|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|disease:Autosomal recessive cutis laxa type 2A|disease staging:before the gross morphological phenotype becomes apparent|genetic modification:gene knock out|genotype:atp6v1e1b cmg78/cmg78|individual:pool of 10 larvae|organism part:whole organism|phenotype:atp6v1e1b deletion|replicate:biological replicate|sample name:E MTAB 8824:atp6v1e1b cmg78/cmg78 1|scientific name:Danio rerio|sex:male|strain:AB                 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E MTAB 8824:atp6v1e1b cmg78/cmg78 1 p atp6v1e1b cmg78/cmg78 1 p RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. Experimental Factor: genotype:atp6v1e1b cmg78/cmg78|Experimental Factor: disease:Autosomal recessive cutis laxa type 2A RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 3000   ERP120207 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26 atp6v1e1b_cmg78cmg78_1_R1.fastq.gz atp6v1e1b_cmg78cmg78_1_R2.fastq.gz fastq fastq 12414679741.0 42312611.0 E MTAB 8824:atp6v1e1b cmg78cmg78 1 R 0:146.73 1:146.67 A:3241482438;C:2955264087;G:2942821679;T:3271073016;N:4038521 146 146     3241482438 2955264087 2942821679 3271073016 4038521 ERX3965605 ERS4355888 ERA2393549 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive 2 0.94874 0.94968 0.05959 0.05739 0.66965 0.67706 0.46769 0.45932 67 67 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2020-02-26 Larval Larval Whole Organism All anatomical structures
9822 9822 ERR3957800 ERX3965604 ERS4355887 ERP120207 PRJEB36940 RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E-MTAB-8824 Transcriptome Analysis Cutis laxa CL syndromes are a heterogenous group of connective tissue disorders that share a loose redundant skin as a common clinical feature. The systemic features vary among the different subtypes. CL is caused by mutations in genes encoding for components of the extracellular matrix FBLN4 FBLN5 LTBP4 and ELN encoding for elastin modifying enzymes ATP7A or encoding for components that influence cellular trafficking and metabolism ATP6V1E1 ATP6V1A ATP6V0A2 ALDH18A1 RIN2 GORAB PYCR1 and SLC2A10. ATP6V1E1–related CL cause loose redundant skin folds variable mental disability typical facial characteristics lipodystrophy hypotonia and cardiopulmonary involvement including pneumothorax hypertrophic cardiomyopathy and aortic root dilatation. The intent of this study is to investigate which genes are up or downregulated in atp6v1e1b deficient zebrafish larvae compared to wild type controls. Via transcriptome analysis we want to study the pathogenic mechanism of ATP6V1E1 induced CL syndrome. We use a zebrafish line with viral insertion in the five primeUTR of atp6v1e1b disrupting transcription atp6v1e1bhi577aTg/+ from the Zebrafish International Research Center ZIRC and we use a line harboring a two base pair insertion followed by a three base pair deletion in exon 5 of atp6v1e1b c.334insGG; c.337 340delCGG predicted to result in p.R111WfsX2 atp6v1e1bcmg78/+ which we created ourselves by CRISPR Cas9 mutagenesis. Overview of the experimental work flow: Sample collection: pool of 10 zebrafish larvae of 3 dpf/genotype in RNA later RNA extraction: TRIzol® Reagent RNeasy mini kit Qiagen according to manufacturer's instructions RNA integrity: 2100 Bioanalyzer Agilent Sequencing library: TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina Sequencing: HiSeq 3000 sequencer Illumina paired end 150 bp sequencing facility of the Center of Medical Genetics Ghent alignement to zebrafish GRCz10 reference g… ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26   Protocols: Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. atp6v1e1b +/+ 3 SAMEA6591593 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University ENA FIRST PUBLIC:2020 08 03T04:04:15Z|ENA LAST UPDATE:2020 02 26T13:29:53Z|External Id:SAMEA6591593|INSDC center name:Center for Medical Genetics Ghent Ghent University Hospital Ghent Belgium Department of biomolecular medicine Ghent University|INSDC first public:2020 08 03T04:04:15Z|INSDC last update:2020 02 26T13:29:53Z|INSDC status:public|Submitter Id:E MTAB 8824:atp6v1e1b +/+ 3|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|disease:normal|genotype:atp6v1e1b +/+|individual:pool of 10 larvae|organism part:whole organism|phenotype:wild type|replicate:biological replicate|sample name:E MTAB 8824:atp6v1e1b +/+ 3|scientific name:Danio rerio|sex:male|strain:AB                 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E MTAB 8824:atp6v1e1b +/+ 3 p atp6v1e1b +/+ 3 p RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. Experimental Factor: genotype:atp6v1e1b +/+|Experimental Factor: disease:normal RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 3000   ERP120207 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26 atp6v1e1b_wt_3_R1.fastq.gz atp6v1e1b_wt_3_R2.fastq.gz fastq fastq 10732686810.0 36678487.0 E MTAB 8824:atp6v1e1b wt 3 R 0:146.35 1:146.27 A:2811732736;C:2549901549;G:2519402587;T:2850106740;N:1543198 146 146     2811732736 2549901549 2519402587 2850106740 1543198 ERX3965604 ERS4355887 ERA2393549 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive 2 0.94597 0.94583 0.06262 0.05884 0.66811 0.67623 0.46245 0.46395 151 150 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2020-02-26 Larval Larval Whole Organism All anatomical structures
9823 9823 ERR3957799 ERX3965603 ERS4355886 ERP120207 PRJEB36940 RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E-MTAB-8824 Transcriptome Analysis Cutis laxa CL syndromes are a heterogenous group of connective tissue disorders that share a loose redundant skin as a common clinical feature. The systemic features vary among the different subtypes. CL is caused by mutations in genes encoding for components of the extracellular matrix FBLN4 FBLN5 LTBP4 and ELN encoding for elastin modifying enzymes ATP7A or encoding for components that influence cellular trafficking and metabolism ATP6V1E1 ATP6V1A ATP6V0A2 ALDH18A1 RIN2 GORAB PYCR1 and SLC2A10. ATP6V1E1–related CL cause loose redundant skin folds variable mental disability typical facial characteristics lipodystrophy hypotonia and cardiopulmonary involvement including pneumothorax hypertrophic cardiomyopathy and aortic root dilatation. The intent of this study is to investigate which genes are up or downregulated in atp6v1e1b deficient zebrafish larvae compared to wild type controls. Via transcriptome analysis we want to study the pathogenic mechanism of ATP6V1E1 induced CL syndrome. We use a zebrafish line with viral insertion in the five primeUTR of atp6v1e1b disrupting transcription atp6v1e1bhi577aTg/+ from the Zebrafish International Research Center ZIRC and we use a line harboring a two base pair insertion followed by a three base pair deletion in exon 5 of atp6v1e1b c.334insGG; c.337 340delCGG predicted to result in p.R111WfsX2 atp6v1e1bcmg78/+ which we created ourselves by CRISPR Cas9 mutagenesis. Overview of the experimental work flow: Sample collection: pool of 10 zebrafish larvae of 3 dpf/genotype in RNA later RNA extraction: TRIzol® Reagent RNeasy mini kit Qiagen according to manufacturer's instructions RNA integrity: 2100 Bioanalyzer Agilent Sequencing library: TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina Sequencing: HiSeq 3000 sequencer Illumina paired end 150 bp sequencing facility of the Center of Medical Genetics Ghent alignement to zebrafish GRCz10 reference g… ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26   Protocols: Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. atp6v1e1b +/+ 2 SAMEA6591592 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University ENA FIRST PUBLIC:2020 08 03T04:04:15Z|ENA LAST UPDATE:2020 02 26T13:29:53Z|External Id:SAMEA6591592|INSDC center name:Center for Medical Genetics Ghent Ghent University Hospital Ghent Belgium Department of biomolecular medicine Ghent University|INSDC first public:2020 08 03T04:04:15Z|INSDC last update:2020 02 26T13:29:53Z|INSDC status:public|Submitter Id:E MTAB 8824:atp6v1e1b +/+ 2|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|disease:normal|genotype:atp6v1e1b +/+|individual:pool of 10 larvae|organism part:whole organism|phenotype:wild type|replicate:biological replicate|sample name:E MTAB 8824:atp6v1e1b +/+ 2|scientific name:Danio rerio|sex:male|strain:AB                 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E MTAB 8824:atp6v1e1b +/+ 2 p atp6v1e1b +/+ 2 p RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. Experimental Factor: genotype:atp6v1e1b +/+|Experimental Factor: disease:normal RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 3000   ERP120207 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26 atp6v1e1b_wt_2_R1.fastq.gz atp6v1e1b_wt_2_R2.fastq.gz fastq fastq 12727487811.0 43201570.0 E MTAB 8824:atp6v1e1b wt 2 R 0:147.34 1:147.26 A:3340874575;C:3010888750;G:2998295317;T:3376023714;N:1405455 147 147     3340874575 3010888750 2998295317 3376023714 1405455 ERX3965603 ERS4355886 ERA2393549 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive 2 0.95099 0.95093 0.06372 0.06035 0.66983 0.6773 0.46418 0.47128 150 151 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2020-02-26 Larval Larval Whole Organism All anatomical structures
9824 9824 ERR3957798 ERX3965602 ERS4355885 ERP120207 PRJEB36940 RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E-MTAB-8824 Transcriptome Analysis Cutis laxa CL syndromes are a heterogenous group of connective tissue disorders that share a loose redundant skin as a common clinical feature. The systemic features vary among the different subtypes. CL is caused by mutations in genes encoding for components of the extracellular matrix FBLN4 FBLN5 LTBP4 and ELN encoding for elastin modifying enzymes ATP7A or encoding for components that influence cellular trafficking and metabolism ATP6V1E1 ATP6V1A ATP6V0A2 ALDH18A1 RIN2 GORAB PYCR1 and SLC2A10. ATP6V1E1–related CL cause loose redundant skin folds variable mental disability typical facial characteristics lipodystrophy hypotonia and cardiopulmonary involvement including pneumothorax hypertrophic cardiomyopathy and aortic root dilatation. The intent of this study is to investigate which genes are up or downregulated in atp6v1e1b deficient zebrafish larvae compared to wild type controls. Via transcriptome analysis we want to study the pathogenic mechanism of ATP6V1E1 induced CL syndrome. We use a zebrafish line with viral insertion in the five primeUTR of atp6v1e1b disrupting transcription atp6v1e1bhi577aTg/+ from the Zebrafish International Research Center ZIRC and we use a line harboring a two base pair insertion followed by a three base pair deletion in exon 5 of atp6v1e1b c.334insGG; c.337 340delCGG predicted to result in p.R111WfsX2 atp6v1e1bcmg78/+ which we created ourselves by CRISPR Cas9 mutagenesis. Overview of the experimental work flow: Sample collection: pool of 10 zebrafish larvae of 3 dpf/genotype in RNA later RNA extraction: TRIzol® Reagent RNeasy mini kit Qiagen according to manufacturer's instructions RNA integrity: 2100 Bioanalyzer Agilent Sequencing library: TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina Sequencing: HiSeq 3000 sequencer Illumina paired end 150 bp sequencing facility of the Center of Medical Genetics Ghent alignement to zebrafish GRCz10 reference g… ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26   Protocols: Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. atp6v1e1b +/+ 1 SAMEA6591591 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University ENA FIRST PUBLIC:2020 08 03T04:04:15Z|ENA LAST UPDATE:2020 02 26T13:29:53Z|External Id:SAMEA6591591|INSDC center name:Center for Medical Genetics Ghent Ghent University Hospital Ghent Belgium Department of biomolecular medicine Ghent University|INSDC first public:2020 08 03T04:04:15Z|INSDC last update:2020 02 26T13:29:53Z|INSDC status:public|Submitter Id:E MTAB 8824:atp6v1e1b +/+ 1|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|disease:normal|genotype:atp6v1e1b +/+|individual:pool of 10 larvae|organism part:whole organism|phenotype:wild type|replicate:biological replicate|sample name:E MTAB 8824:atp6v1e1b +/+ 1|scientific name:Danio rerio|sex:male|strain:AB                 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls E MTAB 8824:atp6v1e1b +/+ 1 p atp6v1e1b +/+ 1 p RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina San Diego California United States supplemented with TruSeq® RNA Single Indexes Set A Illumina. Experimental Factor: genotype:atp6v1e1b +/+|Experimental Factor: disease:normal RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 3000   ERP120207 Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26 atp6v1e1b_wt_1_R1.fastq.gz atp6v1e1b_wt_1_R2.fastq.gz fastq fastq 12570351660.0 42959340.0 E MTAB 8824:atp6v1e1b wt 1 R 0:146.34 1:146.27 A:3284633072;C:2995010895;G:2959080366;T:3328876226;N:2751101 146 146     3284633072 2995010895 2959080366 3328876226 2751101 ERX3965602 ERS4355885 ERA2393549 Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive 2 0.95027 0.95086 0.06766 0.06493 0.66667 0.6747 0.46208 0.46879 150 151 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Belgium 2020-02-26 Larval Larval Whole Organism All anatomical structures
9862 9862 ERR4091982 ERX4087483 ERS4539485 ERP121491 PRJEB38108 RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E-MTAB-9018 Transcriptome Analysis Wilt type and somatostatin 3 Sst3 gene CrispR/Cas9 mutants of the AB zebrafish strain were treated with dextran sodium sulfate DSS to determine the role of sst3 in the innate immune response. ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01   Protocols: Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferen… Sample 9 SAMEA6811839 Centre of Marine Sciences ENA FIRST PUBLIC:2020 07 31T04:03:56Z|ENA LAST UPDATE:2020 05 01T13:37:30Z|External Id:SAMEA6811839|INSDC center name:Centre of Marine Sciences|INSDC first public:2020 07 31T04:03:56Z|INSDC last update:2020 05 01T13:37:30Z|INSDC status:public|Submitter Id:E MTAB 9018:Sample 9|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool of 10 individuals 9|sample name:E MTAB 9018:Sample 9|scientific name:Danio rerio|strain:AB                 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E MTAB 9018:Sample 9 p Sample 9 p RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially … Experimental Factor: genotype:wild type genotype|Experimental Factor: stimulus:n1 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP121491 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01 W_Con_C_1.fq.gz W_Con_C_2.fq.gz fastq fastq 7774714800.0 25915716.0 E MTAB 9018:W Con C 0:150 1:150 A:2077915893;C:1835776410;G:1813929552;T:2046850194;N:242751 150 150     2077915893 1835776410 1813929552 2046850194 242751 ERX4087483 ERS4539485 ERA2539869 European Nucleotide Archive European Nucleotide Archive 2 0.95247 0.95115 0.09117 0.09111 0.67048 0.67188 0.46883 0.46977 150 150 B B biological fallback assumption illumina hiseq_era 3prime poly_a nebnext bulk unknown unknown   Unknown 2020-05-01 Larval Larval Whole Organism All anatomical structures
9863 9863 ERR4091981 ERX4087482 ERS4539484 ERP121491 PRJEB38108 RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E-MTAB-9018 Transcriptome Analysis Wilt type and somatostatin 3 Sst3 gene CrispR/Cas9 mutants of the AB zebrafish strain were treated with dextran sodium sulfate DSS to determine the role of sst3 in the innate immune response. ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01   Protocols: Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferen… Sample 8 SAMEA6811838 Centre of Marine Sciences ENA FIRST PUBLIC:2020 07 31T04:03:56Z|ENA LAST UPDATE:2020 05 01T13:37:30Z|External Id:SAMEA6811838|INSDC center name:Centre of Marine Sciences|INSDC first public:2020 07 31T04:03:56Z|INSDC last update:2020 05 01T13:37:30Z|INSDC status:public|Submitter Id:E MTAB 9018:Sample 8|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool of 10 individuals 8|sample name:E MTAB 9018:Sample 8|scientific name:Danio rerio|strain:AB                 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E MTAB 9018:Sample 8 p Sample 8 p RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially … Experimental Factor: genotype:wild type genotype|Experimental Factor: stimulus:n1 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP121491 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01 W_Con_B_1.fq.gz W_Con_B_2.fq.gz fastq fastq 7020462600.0 23401542.0 E MTAB 9018:W Con B 0:150 1:150 A:1871589307;C:1660051922;G:1642143183;T:1846464462;N:213726 150 150     1871589307 1660051922 1642143183 1846464462 213726 ERX4087482 ERS4539484 ERA2539869 European Nucleotide Archive European Nucleotide Archive 2 0.95469 0.95135 0.08748 0.08735 0.67251 0.6744 0.47258 0.47123 150 150 B B biological fallback assumption illumina hiseq_era 3prime poly_a nebnext bulk unknown unknown   Unknown 2020-05-01 Larval Larval Whole Organism All anatomical structures
9864 9864 ERR4091980 ERX4087481 ERS4539483 ERP121491 PRJEB38108 RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E-MTAB-9018 Transcriptome Analysis Wilt type and somatostatin 3 Sst3 gene CrispR/Cas9 mutants of the AB zebrafish strain were treated with dextran sodium sulfate DSS to determine the role of sst3 in the innate immune response. ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01   Protocols: Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferen… Sample 7 SAMEA6811837 Centre of Marine Sciences ENA FIRST PUBLIC:2020 07 31T04:03:56Z|ENA LAST UPDATE:2020 05 01T13:37:30Z|External Id:SAMEA6811837|INSDC center name:Centre of Marine Sciences|INSDC first public:2020 07 31T04:03:56Z|INSDC last update:2020 05 01T13:37:30Z|INSDC status:public|Submitter Id:E MTAB 9018:Sample 7|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool of 10 individuals 7|sample name:E MTAB 9018:Sample 7|scientific name:Danio rerio|strain:AB                 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E MTAB 9018:Sample 7 p Sample 7 p RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially … Experimental Factor: genotype:wild type genotype|Experimental Factor: stimulus:n1 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP121491 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01 W_Con_A_1.fq.gz W_Con_A_2.fq.gz fastq fastq 8519130900.0 28397103.0 E MTAB 9018:W Con A 0:150 1:150 A:2274905972;C:2012378249;G:1988658778;T:2242930152;N:257749 150 150     2274905972 2012378249 1988658778 2242930152 257749 ERX4087481 ERS4539483 ERA2539869 European Nucleotide Archive European Nucleotide Archive 2 0.95188 0.94559 0.09538 0.09461 0.66354 0.66513 0.47016 0.46912 150 150 B B biological fallback assumption illumina hiseq_era 3prime poly_a nebnext bulk unknown unknown   Unknown 2020-05-01 Larval Larval Whole Organism All anatomical structures
9865 9865 ERR4091979 ERX4087480 ERS4539482 ERP121491 PRJEB38108 RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E-MTAB-9018 Transcriptome Analysis Wilt type and somatostatin 3 Sst3 gene CrispR/Cas9 mutants of the AB zebrafish strain were treated with dextran sodium sulfate DSS to determine the role of sst3 in the innate immune response. ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01   Protocols: Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferen… Sample 6 SAMEA6811836 Centre of Marine Sciences ENA FIRST PUBLIC:2020 07 31T04:03:56Z|ENA LAST UPDATE:2020 05 01T13:37:30Z|External Id:SAMEA6811836|INSDC center name:Centre of Marine Sciences|INSDC first public:2020 07 31T04:03:56Z|INSDC last update:2020 05 01T13:37:30Z|INSDC status:public|Submitter Id:E MTAB 9018:Sample 6|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:CRISPR/Cas9 mediated Sst3 / knockout|individual:pool of 10 individuals 6|sample name:E MTAB 9018:Sample 6|scientific name:Danio rerio|strain:AB                 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E MTAB 9018:Sample 6 p Sample 6 p RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially … Experimental Factor: genotype:CRISPR/Cas9 mediated Sst3 / knockout|Experimental Factor: stimulus:dextran sodium sulfate sodium 0.4% RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP121491 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01 M_DSS_C_1.fq.gz M_DSS_C_2.fq.gz fastq fastq 8624526600.0 28748422.0 E MTAB 9018:M DSS C 0:150 1:150 A:2329218271;C:2003670989;G:1988245153;T:2303170674;N:221513 150 150     2329218271 2003670989 1988245153 2303170674 221513 ERX4087480 ERS4539482 ERA2539869 European Nucleotide Archive European Nucleotide Archive 2 0.94319 0.9419 0.11569 0.11535 0.65429 0.65425 0.47566 0.4769 150 150 B B biological fallback assumption illumina hiseq_era 3prime poly_a nebnext bulk unknown unknown   Unknown 2020-05-01 Larval Larval Whole Organism All anatomical structures
9866 9866 ERR4091978 ERX4087479 ERS4539481 ERP121491 PRJEB38108 RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E-MTAB-9018 Transcriptome Analysis Wilt type and somatostatin 3 Sst3 gene CrispR/Cas9 mutants of the AB zebrafish strain were treated with dextran sodium sulfate DSS to determine the role of sst3 in the innate immune response. ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01   Protocols: Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferen… Sample 5 SAMEA6811835 Centre of Marine Sciences ENA FIRST PUBLIC:2020 07 31T04:03:56Z|ENA LAST UPDATE:2020 05 01T13:37:30Z|External Id:SAMEA6811835|INSDC center name:Centre of Marine Sciences|INSDC first public:2020 07 31T04:03:56Z|INSDC last update:2020 05 01T13:37:30Z|INSDC status:public|Submitter Id:E MTAB 9018:Sample 5|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:CRISPR/Cas9 mediated Sst3 / knockout|individual:pool of 10 individuals 5|sample name:E MTAB 9018:Sample 5|scientific name:Danio rerio|strain:AB                 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E MTAB 9018:Sample 5 p Sample 5 p RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially … Experimental Factor: genotype:CRISPR/Cas9 mediated Sst3 / knockout|Experimental Factor: stimulus:dextran sodium sulfate sodium 0.4% RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP121491 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01 M_DSS_B_1.fq.gz M_DSS_B_2.fq.gz fastq fastq 7724861100.0 25749537.0 E MTAB 9018:M DSS B 0:150 1:150 A:2075007992;C:1808741476;G:1794964692;T:2045949533;N:197407 150 150     2075007992 1808741476 1794964692 2045949533 197407 ERX4087479 ERS4539481 ERA2539869 European Nucleotide Archive European Nucleotide Archive 2 0.94579 0.94493 0.10589 0.10529 0.65464 0.65628 0.47753 0.4801 150 150 B B biological fallback assumption illumina hiseq_era 3prime poly_a nebnext bulk unknown unknown   Unknown 2020-05-01 Larval Larval Whole Organism All anatomical structures
9867 9867 ERR4091977 ERX4087478 ERS4539480 ERP121491 PRJEB38108 RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E-MTAB-9018 Transcriptome Analysis Wilt type and somatostatin 3 Sst3 gene CrispR/Cas9 mutants of the AB zebrafish strain were treated with dextran sodium sulfate DSS to determine the role of sst3 in the innate immune response. ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01   Protocols: Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferen… Sample 4 SAMEA6811834 Centre of Marine Sciences ENA FIRST PUBLIC:2020 07 31T04:03:56Z|ENA LAST UPDATE:2020 05 01T13:37:30Z|External Id:SAMEA6811834|INSDC center name:Centre of Marine Sciences|INSDC first public:2020 07 31T04:03:56Z|INSDC last update:2020 05 01T13:37:30Z|INSDC status:public|Submitter Id:E MTAB 9018:Sample 4|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:CRISPR/Cas9 mediated Sst3 / knockout|individual:pool of 10 individuals 4|sample name:E MTAB 9018:Sample 4|scientific name:Danio rerio|strain:AB                 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E MTAB 9018:Sample 4 p Sample 4 p RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially … Experimental Factor: genotype:CRISPR/Cas9 mediated Sst3 / knockout|Experimental Factor: stimulus:dextran sodium sulfate sodium 0.4% RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP121491 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01 M_DSS_A_1.fq.gz M_DSS_A_2.fq.gz fastq fastq 7688293800.0 25627646.0 E MTAB 9018:M DSS A 0:150 1:150 A:2073022052;C:1791469708;G:1778836919;T:2044769558;N:195563 150 150     2073022052 1791469708 1778836919 2044769558 195563 ERX4087478 ERS4539480 ERA2539869 European Nucleotide Archive European Nucleotide Archive 2 0.9469 0.94648 0.09843 0.09883 0.65646 0.65681 0.4755 0.47342 150 150 B B biological fallback assumption illumina hiseq_era 3prime poly_a nebnext bulk unknown unknown   Unknown 2020-05-01 Larval Larval Whole Organism All anatomical structures
9868 9868 ERR4091976 ERX4087477 ERS4539479 ERP121491 PRJEB38108 RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E-MTAB-9018 Transcriptome Analysis Wilt type and somatostatin 3 Sst3 gene CrispR/Cas9 mutants of the AB zebrafish strain were treated with dextran sodium sulfate DSS to determine the role of sst3 in the innate immune response. ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01   Protocols: Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferen… Sample 3 SAMEA6811833 Centre of Marine Sciences ENA FIRST PUBLIC:2020 07 31T04:03:56Z|ENA LAST UPDATE:2020 05 01T13:37:30Z|External Id:SAMEA6811833|INSDC center name:Centre of Marine Sciences|INSDC first public:2020 07 31T04:03:56Z|INSDC last update:2020 05 01T13:37:30Z|INSDC status:public|Submitter Id:E MTAB 9018:Sample 3|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:CRISPR/Cas9 mediated Sst3 / knockout|individual:pool of 10 individuals 3|sample name:E MTAB 9018:Sample 3|scientific name:Danio rerio|strain:AB                 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E MTAB 9018:Sample 3 p Sample 3 p RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially … Experimental Factor: genotype:CRISPR/Cas9 mediated Sst3 / knockout|Experimental Factor: stimulus:n1 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP121491 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01 M_Con_C_1.fq.gz M_Con_C_2.fq.gz fastq fastq 7985140200.0 26617134.0 E MTAB 9018:M Con C 0:150 1:150 A:2144760983;C:1867900138;G:1849556035;T:2122718629;N:204415 150 150     2144760983 1867900138 1849556035 2122718629 204415 ERX4087477 ERS4539479 ERA2539869 European Nucleotide Archive European Nucleotide Archive 2 0.94683 0.94599 0.10169 0.10188 0.66356 0.66306 0.46315 0.46572 150 150 B B biological fallback assumption illumina hiseq_era 3prime poly_a nebnext bulk unknown unknown   Unknown 2020-05-01 Larval Larval Whole Organism All anatomical structures
9869 9869 ERR4091975 ERX4087476 ERS4539478 ERP121491 PRJEB38108 RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E-MTAB-9018 Transcriptome Analysis Wilt type and somatostatin 3 Sst3 gene CrispR/Cas9 mutants of the AB zebrafish strain were treated with dextran sodium sulfate DSS to determine the role of sst3 in the innate immune response. ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01   Protocols: Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferen… Sample 2 SAMEA6811832 Centre of Marine Sciences ENA FIRST PUBLIC:2020 07 31T04:03:56Z|ENA LAST UPDATE:2020 05 01T13:37:30Z|External Id:SAMEA6811832|INSDC center name:Centre of Marine Sciences|INSDC first public:2020 07 31T04:03:56Z|INSDC last update:2020 05 01T13:37:30Z|INSDC status:public|Submitter Id:E MTAB 9018:Sample 2|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:CRISPR/Cas9 mediated Sst3 / knockout|individual:pool of 10 individuals 2|sample name:E MTAB 9018:Sample 2|scientific name:Danio rerio|strain:AB                 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E MTAB 9018:Sample 2 p Sample 2 p RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially … Experimental Factor: genotype:CRISPR/Cas9 mediated Sst3 / knockout|Experimental Factor: stimulus:n1 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP121491 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01 M_Con_B_1.fq.gz M_Con_B_2.fq.gz fastq fastq 8095952100.0 26986507.0 E MTAB 9018:M Con B 0:150 1:150 A:2169930042;C:1900258308;G:1882602069;T:2142957387;N:204294 150 150     2169930042 1900258308 1882602069 2142957387 204294 ERX4087476 ERS4539478 ERA2539869 European Nucleotide Archive European Nucleotide Archive 2 0.94617 0.94593 0.10478 0.10447 0.66318 0.66336 0.46803 0.46642 150 150 B B biological fallback assumption illumina hiseq_era 3prime poly_a nebnext bulk unknown unknown   Unknown 2020-05-01 Larval Larval Whole Organism All anatomical structures
9870 9870 ERR4091974 ERX4087475 ERS4539477 ERP121491 PRJEB38108 RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E-MTAB-9018 Transcriptome Analysis Wilt type and somatostatin 3 Sst3 gene CrispR/Cas9 mutants of the AB zebrafish strain were treated with dextran sodium sulfate DSS to determine the role of sst3 in the innate immune response. ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01   Protocols: Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferen… Sample 12 SAMEA6811831 Centre of Marine Sciences ENA FIRST PUBLIC:2020 07 31T04:03:56Z|ENA LAST UPDATE:2020 05 01T13:37:30Z|External Id:SAMEA6811831|INSDC center name:Centre of Marine Sciences|INSDC first public:2020 07 31T04:03:56Z|INSDC last update:2020 05 01T13:37:30Z|INSDC status:public|Submitter Id:E MTAB 9018:Sample 12|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool of 10 individuals 12|sample name:E MTAB 9018:Sample 12|scientific name:Danio rerio|strain:AB                 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E MTAB 9018:Sample 12 p Sample 12 p RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially … Experimental Factor: genotype:wild type genotype|Experimental Factor: stimulus:dextran sodium sulfate sodium 0.4% RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP121491 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01 W_DSS_C_1.fq.gz W_DSS_C_2.fq.gz fastq fastq 10705849200.0 35686164.0 E MTAB 9018:W DSS C 0:150 1:150 A:2887224637;C:2496155337;G:2470575601;T:2851559752;N:333873 150 150     2887224637 2496155337 2470575601 2851559752 333873 ERX4087475 ERS4539477 ERA2539869 European Nucleotide Archive European Nucleotide Archive 2 0.94507 0.94439 0.11279 0.11333 0.6561 0.65632 0.47737 0.4743 150 150 B B biological fallback assumption illumina hiseq_era 3prime poly_a nebnext bulk unknown unknown   Unknown 2020-05-01 Larval Larval Whole Organism All anatomical structures
9871 9871 ERR4091973 ERX4087474 ERS4539476 ERP121491 PRJEB38108 RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E-MTAB-9018 Transcriptome Analysis Wilt type and somatostatin 3 Sst3 gene CrispR/Cas9 mutants of the AB zebrafish strain were treated with dextran sodium sulfate DSS to determine the role of sst3 in the innate immune response. ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01   Protocols: Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferen… Sample 11 SAMEA6811830 Centre of Marine Sciences ENA FIRST PUBLIC:2020 07 31T04:03:56Z|ENA LAST UPDATE:2020 05 01T13:37:30Z|External Id:SAMEA6811830|INSDC center name:Centre of Marine Sciences|INSDC first public:2020 07 31T04:03:56Z|INSDC last update:2020 05 01T13:37:30Z|INSDC status:public|Submitter Id:E MTAB 9018:Sample 11|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool of 10 individuals 11|sample name:E MTAB 9018:Sample 11|scientific name:Danio rerio|strain:AB                 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E MTAB 9018:Sample 11 p Sample 11 p RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially … Experimental Factor: genotype:wild type genotype|Experimental Factor: stimulus:dextran sodium sulfate sodium 0.4% RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP121491 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01 W_DSS_B_1.fq.gz W_DSS_B_2.fq.gz fastq fastq 8261533500.0 27538445.0 E MTAB 9018:W DSS B 0:150 1:150 A:2215705349;C:1941946411;G:1919702407;T:2183928810;N:250523 150 150     2215705349 1941946411 1919702407 2183928810 250523 ERX4087474 ERS4539476 ERA2539869 European Nucleotide Archive European Nucleotide Archive 2 0.95069 0.94994 0.09908 0.09883 0.65543 0.65815 0.46658 0.46319 150 150 B B biological fallback assumption illumina hiseq_era 3prime poly_a nebnext bulk unknown unknown   Unknown 2020-05-01 Larval Larval Whole Organism All anatomical structures
9872 9872 ERR4091972 ERX4087473 ERS4539475 ERP121491 PRJEB38108 RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E-MTAB-9018 Transcriptome Analysis Wilt type and somatostatin 3 Sst3 gene CrispR/Cas9 mutants of the AB zebrafish strain were treated with dextran sodium sulfate DSS to determine the role of sst3 in the innate immune response. ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01   Protocols: Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferen… Sample 10 SAMEA6811829 Centre of Marine Sciences ENA FIRST PUBLIC:2020 07 31T04:03:56Z|ENA LAST UPDATE:2020 05 01T13:37:30Z|External Id:SAMEA6811829|INSDC center name:Centre of Marine Sciences|INSDC first public:2020 07 31T04:03:56Z|INSDC last update:2020 05 01T13:37:30Z|INSDC status:public|Submitter Id:E MTAB 9018:Sample 10|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool of 10 individuals 10|sample name:E MTAB 9018:Sample 10|scientific name:Danio rerio|strain:AB                 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E MTAB 9018:Sample 10 p Sample 10 p RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially … Experimental Factor: genotype:wild type genotype|Experimental Factor: stimulus:dextran sodium sulfate sodium 0.4% RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP121491 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01 W_DSS_A_1.fq.gz W_DSS_A_2.fq.gz fastq fastq 10063144500.0 33543815.0 E MTAB 9018:W DSS A 0:150 1:150 A:2698044368;C:2362461290;G:2339825246;T:2662507903;N:305693 150 150     2698044368 2362461290 2339825246 2662507903 305693 ERX4087473 ERS4539475 ERA2539869 European Nucleotide Archive European Nucleotide Archive 2 0.94925 0.94247 0.10432 0.10375 0.6592 0.66214 0.47686 0.46792 150 150 B B biological fallback assumption illumina hiseq_era 3prime poly_a nebnext bulk unknown unknown   Unknown 2020-05-01 Larval Larval Whole Organism All anatomical structures
9873 9873 ERR4091971 ERX4087472 ERS4539474 ERP121491 PRJEB38108 RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E-MTAB-9018 Transcriptome Analysis Wilt type and somatostatin 3 Sst3 gene CrispR/Cas9 mutants of the AB zebrafish strain were treated with dextran sodium sulfate DSS to determine the role of sst3 in the innate immune response. ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01   Protocols: Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferen… Sample 1 SAMEA6811828 Centre of Marine Sciences ENA FIRST PUBLIC:2020 07 31T04:03:56Z|ENA LAST UPDATE:2020 05 01T13:37:30Z|External Id:SAMEA6811828|INSDC center name:Centre of Marine Sciences|INSDC first public:2020 07 31T04:03:56Z|INSDC last update:2020 05 01T13:37:30Z|INSDC status:public|Submitter Id:E MTAB 9018:Sample 1|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:CRISPR/Cas9 mediated Sst3 / knockout|individual:pool of 10 individuals 1|sample name:E MTAB 9018:Sample 1|scientific name:Danio rerio|strain:AB                 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS E MTAB 9018:Sample 1 p Sample 1 p RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS Each sample consisted of a pool of 10 individuals each of 6 dpf wild type WT and homozygous mutant M sst3 / untreated or treated with dextran sodium sulfate DSS which were were frozen at 80C and stored in liquid nitrogen for RNA extraction and sequencing. Zebrafish embryos were obtained from natural spawning and raised until 1 dpf in an incubator Panasonic MIR 254 PC at 28.5°C in recirculating water 60 μg/mL instant ocean sea salts and supplemented with methylene blue up to 1 dpf. Larvae were grown at 28.5℃ for 5 days and from 6 dpf 15 dpf were fed with Paramecium. RNA from larvae was isolated using TRIzol Invitrogen according to the manufacturer's instructions. The purity of the RNA was assessed using the NanoPhotometer spectrophotometer IMPLEN CA USA and the RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was further assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. Done by Novogene: A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially … Experimental Factor: genotype:CRISPR/Cas9 mediated Sst3 / knockout|Experimental Factor: stimulus:n1 RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA HiSeq X Ten   ERP121491 HiSeq X Ten paired end sequencing; RNA Seq of wilt type and somatostatin 3 CrispR/Cas9 zebrafish mutants treated with dextran sodium sulfate DSS ENA FIRST PUBLIC:2020 07 31|ENA LAST UPDATE:2020 05 01 M_Con_A_1.fq.gz M_Con_A_2.fq.gz fastq fastq 9107946000.0 30359820.0 E MTAB 9018:M Con A 0:150 1:150 A:2399820088;C:2178279512;G:2158247560;T:2371366017;N:232823 150 150     2399820088 2178279512 2158247560 2371366017 232823 ERX4087472 ERS4539474 ERA2539869 European Nucleotide Archive European Nucleotide Archive 2 0.9529 0.95223 0.09148 0.09202 0.66464 0.66569 0.46843 0.46725 150 150 B B biological fallback assumption illumina hiseq_era 3prime poly_a nebnext bulk unknown unknown   Unknown 2020-05-01 Larval Larval Whole Organism All anatomical structures
9874 9874 ERR4132490 ERX4099806 ERS4552001 ERP121652 PRJEB38247 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E-MTAB-9054 Transcriptome Analysis Endocrine disruption can trigger far reaching effects on environmental populations justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing 30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input read counts were normalized with DESeq2 for differential gene expression analysis. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions.… R904 SAMEA6824372 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824372|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R904|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:low exposure|individual:mixed pool of 10 fish|organism part:whole organism|rin values:10|sample name:E MTAB 9054:R904|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E MTAB 9054:R904 s R904 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 h… Experimental Factor: compound:6 propyl 2 thiouracil|Experimental Factor: dose:0.001 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121652 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11 R904_sr.fastq.gz fastq 1605165390.0 31794192.0 E MTAB 9054:R904 0:50.49 1:0 A:412564740;C:388045945;G:374953342;T:427657902;N:1943461 50 0     412564740 388045945 374953342 427657902 1943461 ERX4099806 ERS4552001 ERA2597157 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.93893   0.09893   0.64646   0.47809   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-11 Larval Larval Whole Organism All anatomical structures
9875 9875 ERR4132489 ERX4099805 ERS4552000 ERP121652 PRJEB38247 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E-MTAB-9054 Transcriptome Analysis Endocrine disruption can trigger far reaching effects on environmental populations justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing 30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input read counts were normalized with DESeq2 for differential gene expression analysis. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions.… R900 SAMEA6824371 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824371|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R900|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:low exposure|individual:mixed pool of 10 fish|organism part:whole organism|rin values:9.6|sample name:E MTAB 9054:R900|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E MTAB 9054:R900 s R900 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 h… Experimental Factor: compound:6 propyl 2 thiouracil|Experimental Factor: dose:0.001 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121652 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11 R900_sr.fastq.gz fastq 1597198644.0 31638370.0 E MTAB 9054:R900 0:50.48 1:0 A:410085529;C:386591071;G:373950085;T:424276623;N:2295336 50 0     410085529 386591071 373950085 424276623 2295336 ERX4099805 ERS4552000 ERA2597157 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.93876   0.09801   0.64889   0.48057   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-11 Larval Larval Whole Organism All anatomical structures
9876 9876 ERR4132488 ERX4099804 ERS4551999 ERP121652 PRJEB38247 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E-MTAB-9054 Transcriptome Analysis Endocrine disruption can trigger far reaching effects on environmental populations justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing 30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input read counts were normalized with DESeq2 for differential gene expression analysis. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions.… R896 SAMEA6824370 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824370|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R896|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:low exposure|individual:mixed pool of 10 fish|organism part:whole organism|rin values:10|sample name:E MTAB 9054:R896|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E MTAB 9054:R896 s R896 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 h… Experimental Factor: compound:6 propyl 2 thiouracil|Experimental Factor: dose:0.001 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121652 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11 R896_sr.fastq.gz fastq 1946340744.0 38553341.0 E MTAB 9054:R896 0:50.48 1:0 A:497881336;C:472722708;G:455800573;T:517246014;N:2690113 50 0     497881336 472722708 455800573 517246014 2690113 ERX4099804 ERS4551999 ERA2597157 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.93904   0.10115   0.64885   0.47903   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-11 Larval Larval Whole Organism All anatomical structures
9877 9877 ERR4132487 ERX4099803 ERS4551998 ERP121652 PRJEB38247 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E-MTAB-9054 Transcriptome Analysis Endocrine disruption can trigger far reaching effects on environmental populations justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing 30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input read counts were normalized with DESeq2 for differential gene expression analysis. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions.… R906 SAMEA6824369 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824369|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R906|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:high exposure|individual:mixed pool of 10 fish|organism part:whole organism|rin values:9.8|sample name:E MTAB 9054:R906|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E MTAB 9054:R906 s R906 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 h… Experimental Factor: compound:6 propyl 2 thiouracil|Experimental Factor: dose:0.1 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121652 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11 R906_sr.fastq.gz fastq 2341343751.0 46379726.0 E MTAB 9054:R906 0:50.48 1:0 A:597650493;C:569437401;G:551299383;T:619558551;N:3397923 50 0     597650493 569437401 551299383 619558551 3397923 ERX4099803 ERS4551998 ERA2597157 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.94175   0.09795   0.65153   0.47478   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-11 Larval Larval Whole Organism All anatomical structures
9878 9878 ERR4132486 ERX4099802 ERS4551997 ERP121652 PRJEB38247 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E-MTAB-9054 Transcriptome Analysis Endocrine disruption can trigger far reaching effects on environmental populations justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing 30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input read counts were normalized with DESeq2 for differential gene expression analysis. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions.… R902 SAMEA6824368 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824368|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R902|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:high exposure|individual:mixed pool of 10 fish|organism part:whole organism|rin values:10|sample name:E MTAB 9054:R902|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E MTAB 9054:R902 s R902 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 h… Experimental Factor: compound:6 propyl 2 thiouracil|Experimental Factor: dose:0.1 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121652 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11 R902_sr.fastq.gz fastq 1632244657.0 32331034.0 E MTAB 9054:R902 0:50.49 1:0 A:413710466;C:400183665;G:387130890;T:428954946;N:2264690 50 0     413710466 400183665 387130890 428954946 2264690 ERX4099802 ERS4551997 ERA2597157 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.94282   0.09186   0.65192   0.48446   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-11 Larval Larval Whole Organism All anatomical structures
9879 9879 ERR4132485 ERX4099801 ERS4551996 ERP121652 PRJEB38247 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E-MTAB-9054 Transcriptome Analysis Endocrine disruption can trigger far reaching effects on environmental populations justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing 30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input read counts were normalized with DESeq2 for differential gene expression analysis. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions.… R898 SAMEA6824367 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824367|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R898|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:high exposure|individual:mixed pool of 10 fish|organism part:whole organism|rin values:9.8|sample name:E MTAB 9054:R898|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E MTAB 9054:R898 s R898 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 h… Experimental Factor: compound:6 propyl 2 thiouracil|Experimental Factor: dose:0.1 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121652 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11 R898_sr.fastq.gz fastq 1973588979.0 39097363.0 E MTAB 9054:R898 0:50.48 1:0 A:501700006;C:481059078;G:466931881;T:520778140;N:3119874 50 0     501700006 481059078 466931881 520778140 3119874 ERX4099801 ERS4551996 ERA2597157 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.94133   0.09578   0.651   0.474   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-11 Larval Larval Whole Organism All anatomical structures
9880 9880 ERR4132484 ERX4099800 ERS4551995 ERP121652 PRJEB38247 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E-MTAB-9054 Transcriptome Analysis Endocrine disruption can trigger far reaching effects on environmental populations justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing 30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input read counts were normalized with DESeq2 for differential gene expression analysis. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions.… R903 SAMEA6824366 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824366|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R903|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:normal|individual:mixed pool of 10 fish|organism part:whole organism|rin values:9.8|sample name:E MTAB 9054:R903|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E MTAB 9054:R903 s R903 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 h… Experimental Factor: compound:n1 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121652 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11 R903_sr.fastq.gz fastq 1978975800.0 39199481.0 E MTAB 9054:R903 0:50.48 1:0 A:502614523;C:482986303;G:468168184;T:522608062;N:2598728 50 0     502614523 482986303 468168184 522608062 2598728 ERX4099800 ERS4551995 ERA2597157 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.9404   0.09216   0.64607   0.47417   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-11 Larval Larval Whole Organism All anatomical structures
9881 9881 ERR4132483 ERX4099799 ERS4551994 ERP121652 PRJEB38247 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E-MTAB-9054 Transcriptome Analysis Endocrine disruption can trigger far reaching effects on environmental populations justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing 30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input read counts were normalized with DESeq2 for differential gene expression analysis. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions.… R899 SAMEA6824365 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824365|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R899|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:normal|individual:mixed pool of 10 fish|organism part:whole organism|rin values:10|sample name:E MTAB 9054:R899|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E MTAB 9054:R899 s R899 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 h… Experimental Factor: compound:n1 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121652 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11 R899_sr.fastq.gz fastq 1556233879.0 30835141.0 E MTAB 9054:R899 0:50.47 1:0 A:394448696;C:380284673;G:367546543;T:410802983;N:3150984 50 0     394448696 380284673 367546543 410802983 3150984 ERX4099799 ERS4551994 ERA2597157 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.93845   0.09509   0.64926   0.48436   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-11 Larval Larval Whole Organism All anatomical structures
9882 9882 ERR4132482 ERX4099798 ERS4551993 ERP121652 PRJEB38247 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E-MTAB-9054 Transcriptome Analysis Endocrine disruption can trigger far reaching effects on environmental populations justifying a refusal of market approval for chemicals with ED properties. Ecotoxicogenomic screening was performed to identify molecular fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. 6 Propyl 2 thiouracil 6PTU CAS: 51 52 5 was tested as a model substance for anti thyroidal activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of 6PTU for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked from each sample group and pooled for RNA and protein extraction with NucleoSpin© RNA/Protein kit Macherey Nagel. RNA quality was assessed via a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing 30 million reads per sample. Initial BCL files were demultiplexed to fastq files via bcl2fastq. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library mapped read tables were then merged to a single count matrix. Using this matrix as input read counts were normalized with DESeq2 for differential gene expression analysis. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions.… R895 SAMEA6824364 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 11T17:12:34Z|External Id:SAMEA6824364|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 11T17:12:34Z|INSDC status:public|Submitter Id:E MTAB 9054:R895|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:normal|individual:mixed pool of 10 fish|organism part:whole organism|rin values:10|sample name:E MTAB 9054:R895|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups E MTAB 9054:R895 s R895 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. All samples were extracted on the 09.12.2019. CAS: 51 52 5 Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 h… Experimental Factor: compound:n1 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121652 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of 6 Propyl 2 thiouracil 6 PTU below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 11 R895_sr.fastq.gz fastq 1098959757.0 21771883.0 E MTAB 9054:R895 0:50.48 1:0 A:281414032;C:266978094;G:257304686;T:291591340;N:1671605 50 0     281414032 266978094 257304686 291591340 1671605 ERX4099798 ERS4551993 ERA2597157 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.93996   0.09776   0.64989   0.47968   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-11 Larval Larval Whole Organism All anatomical structures
9883 9883 ERR4140034 ERX4107347 ERS4556110 ERP121678 PRJEB38271 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups E-MTAB-9056 Transcriptome Analysis The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3 CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphologi… R86 SAMEA6828487 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828487|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R86|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:low exposure|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R86|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups E MTAB 9056:R86 s R86 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphological malfo… Experimental Factor: compound:3 3 prime 5 triiodo L thyro9|Experimental Factor: dose:3.3E 06 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121678 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13 R86_sr.fastq.gz fastq 1327826966.0 26294265.0 E MTAB 9056:R86 0:50.50 1:0 A:340934934;C:322947435;G:309801278;T:353159102;N:984217 50 0     340934934 322947435 309801278 353159102 984217 ERX4107347 ERS4556110 ERA2597448 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.9393   0.1031   0.65683   0.46848   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-12 Larval Larval Whole Organism All anatomical structures
9884 9884 ERR4140033 ERX4107346 ERS4556109 ERP121678 PRJEB38271 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups E-MTAB-9056 Transcriptome Analysis The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3 CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphologi… R164 SAMEA6828486 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828486|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R164|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:low exposure|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R164|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups E MTAB 9056:R164 s R164 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphological malfo… Experimental Factor: compound:3 3 prime 5 triiodo L thyro9|Experimental Factor: dose:3.3E 06 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121678 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13 R164_sr.fastq.gz fastq 1513567439.0 29975869.0 E MTAB 9056:R164 0:50.49 1:0 A:388109813;C:368964600;G:352756505;T:402261160;N:1475361 50 0     388109813 368964600 352756505 402261160 1475361 ERX4107346 ERS4556109 ERA2597448 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.93992   0.10282   0.65437   0.47367   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-12 Larval Larval Whole Organism All anatomical structures
9885 9885 ERR4140032 ERX4107345 ERS4556108 ERP121678 PRJEB38271 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups E-MTAB-9056 Transcriptome Analysis The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3 CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphologi… R158 SAMEA6828485 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828485|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R158|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:low exposure|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R158|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups E MTAB 9056:R158 s R158 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphological malfo… Experimental Factor: compound:3 3 prime 5 triiodo L thyro9|Experimental Factor: dose:3.3E 06 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121678 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13 R158_sr.fastq.gz fastq 1512642153.0 29962837.0 E MTAB 9056:R158 0:50.48 1:0 A:389585690;C:365364747;G:351299223;T:404327286;N:2065207 50 0     389585690 365364747 351299223 404327286 2065207 ERX4107345 ERS4556108 ERA2597448 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.93757   0.10553   0.65557   0.47147   49   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-12 Larval Larval Whole Organism All anatomical structures
9886 9886 ERR4140031 ERX4107344 ERS4556107 ERP121678 PRJEB38271 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups E-MTAB-9056 Transcriptome Analysis The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3 CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphologi… R89 SAMEA6828484 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828484|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R89|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:high exposure|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R89|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups E MTAB 9056:R89 s R89 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphological malfo… Experimental Factor: compound:3 3 prime 5 triiodo L thyro9|Experimental Factor: dose:0.000327 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121678 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13 R89_sr.fastq.gz fastq 1347758243.0 26686154.0 E MTAB 9056:R89 0:50.50 1:0 A:347954623;C:326744319;G:311736057;T:360479809;N:843435 50 0     347954623 326744319 311736057 360479809 843435 ERX4107344 ERS4556107 ERA2597448 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.93909   0.1032   0.64906   0.47499   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-12 Larval Larval Whole Organism All anatomical structures
9887 9887 ERR4140030 ERX4107343 ERS4556106 ERP121678 PRJEB38271 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups E-MTAB-9056 Transcriptome Analysis The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3 CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphologi… R167 SAMEA6828483 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828483|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R167|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:high exposure|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R167|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups E MTAB 9056:R167 s R167 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphological malfo… Experimental Factor: compound:3 3 prime 5 triiodo L thyro9|Experimental Factor: dose:0.000327 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121678 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13 R167_sr.fastq.gz fastq 1422756236.0 28174340.0 E MTAB 9056:R167 0:50.50 1:0 A:366380887;C:345824655;G:330108682;T:379312527;N:1129485 50 0     366380887 345824655 330108682 379312527 1129485 ERX4107343 ERS4556106 ERA2597448 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.93724   0.10506   0.65001   0.47599   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-12 Larval Larval Whole Organism All anatomical structures
9888 9888 ERR4140029 ERX4107342 ERS4556105 ERP121678 PRJEB38271 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups E-MTAB-9056 Transcriptome Analysis The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3 CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphologi… R161 SAMEA6828482 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828482|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R161|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:high exposure|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R161|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups E MTAB 9056:R161 s R161 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphological malfo… Experimental Factor: compound:3 3 prime 5 triiodo L thyro9|Experimental Factor: dose:0.000327 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121678 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13 R161_sr.fastq.gz fastq 1696412529.0 33592555.0 E MTAB 9056:R161 0:50.50 1:0 A:439133160;C:409023953;G:389977077;T:457053986;N:1224353 50 0     439133160 409023953 389977077 457053986 1224353 ERX4107342 ERS4556105 ERA2597448 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.93609   0.1083   0.6535   0.46658   50   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-12 Larval Larval Whole Organism All anatomical structures
9889 9889 ERR4140028 ERX4107341 ERS4556104 ERP121678 PRJEB38271 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups E-MTAB-9056 Transcriptome Analysis The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3 CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphologi… R85 SAMEA6828481 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828481|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R85|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:control|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R85|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups E MTAB 9056:R85 s R85 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphological malfo… Experimental Factor: compound:n1|Experimental Factor: dose:0 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121678 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13 R85_sr.fastq.gz fastq 1115426084.0 22086160.0 E MTAB 9056:R85 0:50.50 1:0 A:288411880;C:265358022;G:259432943;T:301493661;N:729578 50 0     288411880 265358022 259432943 301493661 729578 ERX4107341 ERS4556104 ERA2597448 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.94238   0.10918   0.65372   0.48727   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-12 Larval Larval Whole Organism All anatomical structures
9890 9890 ERR4140027 ERX4107340 ERS4556103 ERP121678 PRJEB38271 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups E-MTAB-9056 Transcriptome Analysis The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3 CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphologi… R162 SAMEA6828480 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828480|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R162|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:control|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R162|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups E MTAB 9056:R162 s R162 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphological malfo… Experimental Factor: compound:n1|Experimental Factor: dose:0 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121678 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13 R162_sr.fastq.gz fastq 1368462525.0 27098537.0 E MTAB 9056:R162 0:50.50 1:0 A:352965195;C:330975762;G:317956233;T:365598349;N:966986 50 0     352965195 330975762 317956233 365598349 966986 ERX4107340 ERS4556103 ERA2597448 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.93788   0.10812   0.65482   0.47962   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-12 Larval Larval Whole Organism All anatomical structures
9891 9891 ERR4140026 ERX4107339 ERS4556102 ERP121678 PRJEB38271 RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups E-MTAB-9056 Transcriptome Analysis The aim of this sequencing experiment was to screen for ecotoxicogenomic fingerprints for endocrine disrupting chemicals affecting the thyroid system in zebrafish Danio rerio embryos as aquatic vertebrate model and alternative to animal testing. Triiodothyronine T3 CAS: 6893 02 3 was tested as a model substance for thyroidal inducing activity. In a modified version of the zebrafish embryo toxicity test OECD 236 15 fertilized eggs were exposed to two different sub lethal concentrations of T3 for xxx hours under semi static conditions. Each test comprised of a low exposure LE high exposure HE and negative control NC group and was performed in triplicates. At 96 hpf 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2. ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 12   Protocols: For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphologi… R157 SAMEA6828479 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany ENA FIRST PUBLIC:2020 07 31T04:03:57Z|ENA LAST UPDATE:2020 05 12T15:52:19Z|External Id:SAMEA6828479|INSDC center name:Fraunhofer Institute for Molecular Biology and Applied Ecology Applied Ecology and Bioresources Division Schmallenberg Germany Institute of Ecology Evolution and Diversity Goethe University Frankfurt Frankfurt am Main Germany|INSDC first public:2020 07 31T04:03:57Z|INSDC last update:2020 05 12T15:52:19Z|INSDC status:public|Submitter Id:E MTAB 9056:R157|age:96|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 4|genotype:wild type genotype|growth condition:control|individual:pool of 10 fish|organism part:whole organism|sample name:E MTAB 9056:R157|scientific name:Danio rerio|sex:mixed|strain:AB                 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyro9 T3 below acute toxicity levels against untreated control groups E MTAB 9056:R157 s R157 s RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups For each sample 10 dpf 4 dpf zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were picked for all samples they were euthanized at the same time by placing the tubes simultaneously on ice for 10 minutes. Supernatant from the test solutions was carefully removed without xxx the larvae before adding 350µl of RP1 buffer NucleoSpin RNA Protein kit; Macherey Nagel 740933.250 for tissue homogenization. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 15 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 ml of the respective testing solution Control Low exposure High exposure. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected visually and single coagulated eggs were recorded and removed. At 48 hpf overall survival hatch rates morphological malformations and physiological changes were recorded and aged solutions were replaced by fresh aerated test solutions. At 96 hpf again overall survival hatch rates morphological malfo… Experimental Factor: compound:n1|Experimental Factor: dose:0 RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 4000   ERP121678 Illumina HiSeq 4000 sequencing; RNA Seq of zebrafish embryos 96hpf treated with different concentrations of Triiodothyronine T3 below acute toxicity levels against untreated control groups ENA FIRST PUBLIC:2020 09 30|ENA LAST UPDATE:2020 05 13 R157_sr.fastq.gz fastq 1500167669.0 29707076.0 E MTAB 9056:R157 0:50.50 1:0 A:386622926;C:363330639;G:347819057;T:401278075;N:1116972 50 0     386622926 363330639 347819057 401278075 1116972 ERX4107339 ERS4556102 ERA2597448 Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive Fraunhofer Institute for Molecular Biology and Applied Ecology, Applied Ecology and Bioresources Division, Schmallenberg, Germany Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany|European Nucleotide Archive 1 0.93887   0.10641   0.65283   0.46616   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-05-12 Larval Larval Whole Organism All anatomical structures
10008 10008 ERR4648708 ERX4572379 ERS5128759 ERP124248 PRJEB40594 scospondin mutant embryos E-MTAB-9615 Transcriptome Analysis Transcriptome comparison of scospondin mutants embryos with wild type siblings ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30   Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche 15S6 SAMEA7370309 Paris Brain Institute ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370309|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S6|scientific name:Danio rerio|sex:not available|strain:AB                 NextSeq 500 paired end sequencing; scospondin mutant embryos E MTAB 9615:15S6 p 15S6 p scospondin mutant embryos Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche Experimental Factor: genotype:scospondin[icm15] +/+ or +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP124248 NextSeq 500 paired end sequencing; scospondin mutant embryos ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02 15S6_S11_L001_R1_001.fastq.gz 15S6_S11_L001_R2_001.fastq.gz fastq fastq 1591537736.0 10470643.0 E MTAB 9615:15S6 S11 L001 R 0:76 1:76 A:429238832;C:363616036;G:370142973;T:428278902;N:260993 76 76     429238832 363616036 370142973 428278902 260993 ERX4572379 ERS5128759 ERA2937926 Paris Brain Institute|European Nucleotide Archive Paris Brain Institute|European Nucleotide Archive 2 0.94838 0.95275 0.11825 0.11227 0.67263 0.67535 0.47339 0.48683 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   France 2020-09-30 Undetermined Embryo Whole Organism All anatomical structures
10009 10009 ERR4648709 ERX4572379 ERS5128759 ERP124248 PRJEB40594 scospondin mutant embryos E-MTAB-9615 Transcriptome Analysis Transcriptome comparison of scospondin mutants embryos with wild type siblings ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30   Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche 15S6 SAMEA7370309 Paris Brain Institute ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370309|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S6|scientific name:Danio rerio|sex:not available|strain:AB                 NextSeq 500 paired end sequencing; scospondin mutant embryos E MTAB 9615:15S6 p 15S6 p scospondin mutant embryos Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche Experimental Factor: genotype:scospondin[icm15] +/+ or +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP124248 NextSeq 500 paired end sequencing; scospondin mutant embryos ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02 15S6_S11_L002_R1_001.fastq.gz 15S6_S11_L002_R2_001.fastq.gz fastq fastq 1559456464.0 10259582.0 E MTAB 9615:15S6 S11 L002 R 0:76 1:76 A:420535603;C:356234776;G:362907355;T:419528118;N:250612 76 76     420535603 356234776 362907355 419528118 250612 ERX4572379 ERS5128759 ERA2937926 Paris Brain Institute|European Nucleotide Archive Paris Brain Institute|European Nucleotide Archive 2 0.94922 0.95244 0.11903 0.11395 0.66931 0.67233 0.46849 0.48097 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   France 2020-09-30 Undetermined Embryo Whole Organism All anatomical structures
10010 10010 ERR4648710 ERX4572379 ERS5128759 ERP124248 PRJEB40594 scospondin mutant embryos E-MTAB-9615 Transcriptome Analysis Transcriptome comparison of scospondin mutants embryos with wild type siblings ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30   Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche 15S6 SAMEA7370309 Paris Brain Institute ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370309|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S6|scientific name:Danio rerio|sex:not available|strain:AB                 NextSeq 500 paired end sequencing; scospondin mutant embryos E MTAB 9615:15S6 p 15S6 p scospondin mutant embryos Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche Experimental Factor: genotype:scospondin[icm15] +/+ or +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP124248 NextSeq 500 paired end sequencing; scospondin mutant embryos ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02 15S6_S11_L003_R1_001.fastq.gz 15S6_S11_L003_R2_001.fastq.gz fastq fastq 1611815600.0 10604050.0 E MTAB 9615:15S6 S11 L003 R 0:76 1:76 A:434815382;C:368453005;G:374802612;T:433582623;N:161978 76 76     434815382 368453005 374802612 433582623 161978 ERX4572379 ERS5128759 ERA2937926 Paris Brain Institute|European Nucleotide Archive Paris Brain Institute|European Nucleotide Archive 2 0.94878 0.9521 0.11889 0.11284 0.67302 0.67521 0.47879 0.48281 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   France 2020-09-30 Undetermined Embryo Whole Organism All anatomical structures
10011 10011 ERR4648711 ERX4572379 ERS5128759 ERP124248 PRJEB40594 scospondin mutant embryos E-MTAB-9615 Transcriptome Analysis Transcriptome comparison of scospondin mutants embryos with wild type siblings ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30   Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche 15S6 SAMEA7370309 Paris Brain Institute ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370309|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S6|scientific name:Danio rerio|sex:not available|strain:AB                 NextSeq 500 paired end sequencing; scospondin mutant embryos E MTAB 9615:15S6 p 15S6 p scospondin mutant embryos Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche Experimental Factor: genotype:scospondin[icm15] +/+ or +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP124248 NextSeq 500 paired end sequencing; scospondin mutant embryos ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02 15S6_S11_L004_R1_001.fastq.gz 15S6_S11_L004_R2_001.fastq.gz fastq fastq 1587249512.0 10442431.0 E MTAB 9615:15S6 S11 L004 R 0:76 1:76 A:428113406;C:362725542;G:369262476;T:427024700;N:123388 76 76     428113406 362725542 369262476 427024700 123388 ERX4572379 ERS5128759 ERA2937926 Paris Brain Institute|European Nucleotide Archive Paris Brain Institute|European Nucleotide Archive 2 0.94868 0.95237 0.11954 0.1137 0.66888 0.67411 0.48327 0.48573 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   France 2020-09-30 Undetermined Embryo Whole Organism All anatomical structures
10012 10012 ERR4648704 ERX4572378 ERS5128758 ERP124248 PRJEB40594 scospondin mutant embryos E-MTAB-9615 Transcriptome Analysis Transcriptome comparison of scospondin mutants embryos with wild type siblings ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30   Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche 15S5 SAMEA7370308 Paris Brain Institute ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370308|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S5|scientific name:Danio rerio|sex:not available|strain:AB                 NextSeq 500 paired end sequencing; scospondin mutant embryos E MTAB 9615:15S5 p 15S5 p scospondin mutant embryos Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche Experimental Factor: genotype:scospondin[icm15] +/+ or +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP124248 NextSeq 500 paired end sequencing; scospondin mutant embryos ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02 15S5_S7_L001_R1_001.fastq.gz 15S5_S7_L001_R2_001.fastq.gz fastq fastq 1695774928.0 11156414.0 E MTAB 9615:15S5 S7 L001 R 0:76 1:76 A:456096603;C:390987096;G:394091205;T:454321430;N:278594 76 76     456096603 390987096 394091205 454321430 278594 ERX4572378 ERS5128758 ERA2937926 Paris Brain Institute|European Nucleotide Archive Paris Brain Institute|European Nucleotide Archive 2 0.94681 0.9507 0.14362 0.13726 0.67931 0.68087 0.49708 0.49164 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   France 2020-09-30 Undetermined Embryo Whole Organism All anatomical structures
10013 10013 ERR4648705 ERX4572378 ERS5128758 ERP124248 PRJEB40594 scospondin mutant embryos E-MTAB-9615 Transcriptome Analysis Transcriptome comparison of scospondin mutants embryos with wild type siblings ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30   Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche 15S5 SAMEA7370308 Paris Brain Institute ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370308|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S5|scientific name:Danio rerio|sex:not available|strain:AB                 NextSeq 500 paired end sequencing; scospondin mutant embryos E MTAB 9615:15S5 p 15S5 p scospondin mutant embryos Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche Experimental Factor: genotype:scospondin[icm15] +/+ or +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP124248 NextSeq 500 paired end sequencing; scospondin mutant embryos ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02 15S5_S7_L002_R1_001.fastq.gz 15S5_S7_L002_R2_001.fastq.gz fastq fastq 1652445504.0 10871352.0 E MTAB 9615:15S5 S7 L002 R 0:76 1:76 A:444752710;C:381030057;G:383777650;T:442619007;N:266080 76 76     444752710 381030057 383777650 442619007 266080 ERX4572378 ERS5128758 ERA2937926 Paris Brain Institute|European Nucleotide Archive Paris Brain Institute|European Nucleotide Archive 2 0.94649 0.94993 0.14201 0.1357 0.68124 0.68471 0.49354 0.48934 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   France 2020-09-30 Undetermined Embryo Whole Organism All anatomical structures
10014 10014 ERR4648706 ERX4572378 ERS5128758 ERP124248 PRJEB40594 scospondin mutant embryos E-MTAB-9615 Transcriptome Analysis Transcriptome comparison of scospondin mutants embryos with wild type siblings ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30   Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche 15S5 SAMEA7370308 Paris Brain Institute ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370308|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S5|scientific name:Danio rerio|sex:not available|strain:AB                 NextSeq 500 paired end sequencing; scospondin mutant embryos E MTAB 9615:15S5 p 15S5 p scospondin mutant embryos Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche Experimental Factor: genotype:scospondin[icm15] +/+ or +/ RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP124248 NextSeq 500 paired end sequencing; scospondin mutant embryos ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02 15S5_S7_L003_R1_001.fastq.gz 15S5_S7_L003_R2_001.fastq.gz fastq fastq 1721026536.0 11322543.0 E MTAB 9615:15S5 S7 L003 R 0:76 1:76 A:463210590;C:396958291;G:399739948;T:460942070;N:175637 76 76     463210590 396958291 399739948 460942070 175637 ERX4572378 ERS5128758 ERA2937926 Paris Brain Institute|European Nucleotide Archive Paris Brain Institute|European Nucleotide Archive 2 0.94689 0.95134 0.14445 0.13799 0.68083 0.68308 0.4907 0.49184 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   France 2020-09-30 Undetermined Embryo 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");;