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
5026,ERR1706529,ERX1776763,ERS1227000,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 C9,SAMEA4055890,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000051|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055890|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:24:00Z|INSDC status:public|Submitter Id:d7b0b9c0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7b0b9c0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#23,17117131,Illumina sequencing of library 17117131  constructed from sample accession ERS1227000 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence ACTGAT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#23.cram,cram,743861850.0,4959079.0,SC RUN 20417 1#23,0:75 1:75,A:188550455;C:183533703;G:184197810;T:187506925;N:72957,75,75,,,188550455,183533703,184197810,187506925,72957,ERX1776763,ERS1227000,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.96302,0.96531,0.19802,0.19492,0.73298,0.73312,0.57888,0.58087,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5029,ERR1706526,ERX1776760,ERS1226955,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 C1,SAMEA4055845,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000048|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055845|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:23:08Z|INSDC status:public|Submitter Id:d799d660 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d799d660 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#20,17117095,Illumina sequencing of library 17117095  constructed from sample accession ERS1226955 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence GTTTCG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#20.cram,cram,1202223750.0,8014825.0,SC RUN 20417 1#20,0:75 1:75,A:288569721;C:312339594;G:312724314;T:288471735;N:118386,75,75,,,288569721,312339594,312724314,288471735,118386,ERX1776760,ERS1226955,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.9701,0.97208,0.23493,0.2308,0.75856,0.75893,0.51831,0.52827,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5033,ERR1706522,ERX1776756,ERS1226910,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 B6,SAMEA4055800,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000044|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055800|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:22:20Z|INSDC status:public|Submitter Id:d778e0e0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d778e0e0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#16,17117142,Illumina sequencing of library 17117142  constructed from sample accession ERS1226910 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence CCGTCC.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#16.cram,cram,1397786700.0,9318578.0,SC RUN 20417 1#16,0:75 1:75,A:370541493;C:328697895;G:330649047;T:367761875;N:136390,75,75,,,370541493,328697895,330649047,367761875,136390,ERX1776756,ERS1226910,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95779,0.96097,0.15701,0.15529,0.72462,0.72425,0.53437,0.53651,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5034,ERR1706521,ERX1776755,ERS1226903,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 B4,SAMEA4055793,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000043|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055793|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:22:11Z|INSDC status:public|Submitter Id:d7713fc0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7713fc0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#15,17117130,Illumina sequencing of library 17117130  constructed from sample accession ERS1226903 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence ATGTCA.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#15.cram,cram,2090642550.0,13937617.0,SC RUN 20417 1#15,0:75 1:75,A:573574606;C:473115476;G:474137164;T:569607223;N:208081,75,75,,,573574606,473115476,474137164,569607223,208081,ERX1776755,ERS1226903,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95314,0.95602,0.13917,0.13779,0.71605,0.7161,0.5009,0.49877,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5035,ERR1706520,ERX1776754,ERS1226896,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 B3,SAMEA4055786,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000042|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055786|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:22:03Z|INSDC status:public|Submitter Id:d7697790 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7697790 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#14,17117118,Illumina sequencing of library 17117118  constructed from sample accession ERS1226896 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence AGTTCC.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#14.cram,cram,1829182200.0,12194548.0,SC RUN 20417 1#14,0:75 1:75,A:501496169;C:412501773;G:416194477;T:498811651;N:178130,75,75,,,501496169,412501773,416194477,498811651,178130,ERX1776754,ERS1226896,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95118,0.95498,0.14818,0.14602,0.71431,0.71478,0.49278,0.4993,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5036,ERR1706519,ERX1776753,ERS1226884,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 B2,SAMEA4055774,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000041|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055774|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:21:52Z|INSDC status:public|Submitter Id:d761fd80 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d761fd80 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#13,17117106,Illumina sequencing of library 17117106  constructed from sample accession ERS1226884 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence AGTCAA.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#13.cram,cram,969474450.0,6463163.0,SC RUN 20417 1#13,0:75 1:75,A:262909712;C:222419636;G:222543360;T:261505885;N:95857,75,75,,,262909712,222419636,222543360,261505885,95857,ERX1776753,ERS1226884,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95449,0.95866,0.15114,0.14937,0.71437,0.71465,0.51271,0.50858,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5037,ERR1706518,ERX1776752,ERS1226870,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 B1,SAMEA4055760,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000040|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055760|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:21:36Z|INSDC status:public|Submitter Id:d75a3550 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish actin:prl3.1 embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d75a3550 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#12,17117094,Illumina sequencing of library 17117094  constructed from sample accession ERS1226870 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence CTTGTA.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#12.cram,cram,1454862600.0,9699084.0,SC RUN 20417 1#12,0:75 1:75,A:398496982;C:328471618;G:330736633;T:397014742;N:142625,75,75,,,398496982,328471618,330736633,397014742,142625,ERX1776752,ERS1226870,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95557,0.95961,0.13233,0.1312,0.71441,0.71488,0.49023,0.48445,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5038,ERR1706517,ERX1776751,ERS1226860,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 A12,SAMEA4055750,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000039|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055750|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:21:28Z|INSDC status:public|Submitter Id:d7529430 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7529430 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#11,17117082,Illumina sequencing of library 17117082  constructed from sample accession ERS1226860 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence GGCTAC.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#11.cram,cram,1746393900.0,11642626.0,SC RUN 20417 1#11,0:75 1:75,A:431979433;C:441330253;G:441743262;T:431172392;N:168560,75,75,,,431979433,441330253,441743262,431172392,168560,ERX1776751,ERS1226860,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.96506,0.9668,0.22176,0.21891,0.74491,0.74621,0.60192,0.59716,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5039,ERR1706516,ERX1776750,ERS1226849,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 A11,SAMEA4055739,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000038|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055739|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:21:18Z|INSDC status:public|Submitter Id:d74a56d0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d74a56d0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#10,17117070,Illumina sequencing of library 17117070  constructed from sample accession ERS1226849 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence TAGCTT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#10.cram,cram,1489471050.0,9929807.0,SC RUN 20417 1#10,0:75 1:75,A:370582953;C:374410965;G:374249460;T:370079632;N:148040,75,75,,,370582953,374410965,374249460,370079632,148040,ERX1776750,ERS1226849,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.96529,0.96757,0.21607,0.21231,0.74272,0.7432,0.59703,0.6019,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5040,ERR1706515,ERX1776749,ERS1226835,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 A9,SAMEA4055725,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055725|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:21:06Z|INSDC status:public|Submitter Id:d7428ea0 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7428ea0 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#9,17117058,Illumina sequencing of library 17117058  constructed from sample accession ERS1226835 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence GATCAG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#9.cram,cram,812740200.0,5418268.0,SC RUN 20417 1#9,0:75 1:75,A:212802181;C:193901585;G:194345487;T:211612018;N:78929,75,75,,,212802181,193901585,194345487,211612018,78929,ERX1776749,ERS1226835,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95783,0.95996,0.17262,0.1685,0.72413,0.72448,0.53944,0.53954,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5041,ERR1706514,ERX1776748,ERS1226824,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 A8,SAMEA4055714,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000036|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055714|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:20:58Z|INSDC status:public|Submitter Id:d73ac670 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d73ac670 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#8,17117141,Illumina sequencing of library 17117141  constructed from sample accession ERS1226824 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence ACTTGA.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#8.cram,cram,1782401400.0,11882676.0,SC RUN 20417 1#8,0:75 1:75,A:458909593;C:432851102;G:434061292;T:456406952;N:172461,75,75,,,458909593,432851102,434061292,456406952,172461,ERX1776748,ERS1226824,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.96096,0.96367,0.18551,0.18292,0.73413,0.73373,0.56474,0.56438,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
5042,ERR1706513,ERX1776747,ERS1226813,ERP016002,PRJEB14364,Transcriptome profiling of zebrafish actin prl3 1 transgenic embryos,Transcriptome_profiling_of_zebrafish_actin_prl3_1_transgenic_embryos-sc-4266,Transcriptome Analysis,RNA Seq data was generated from RNA of zebrafish actin:prl3.1 transgenic embryos for transcriptional profiling.,ArrayExpress:E ERAD 507,,,zmp ph260 A7,SAMEA4055703,Wellcome Sanger Institute,ArrayExpress DevelopmentalStage:Segmentation:26+somites   Pharyngula:Prim 5   ZFS:0000028   ZFS:0000035|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 10 24|ENA last update:2016 06 28|External Id:SAMEA4055703|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 10 24T16:33:40Z|INSDC last update:2016 06 28T15:20:49Z|INSDC status:public|Submitter Id:d7332550 2e55 11e6 a63e 3c4a9275d6c8|common name:zebrafish|sample description:RNA from a single zebrafish non transgenic actin:prl3.1 sibling embryo plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:d7332550 2e55 11e6 a63e 3c4a9275d6c8|strain:mixed,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,SC EXP 20417 1#7,17117129,Illumina sequencing of library 17117129  constructed from sample accession ERS1226813 for study accession ERP016002.  This is part of an Illumina multiplexed sequencing run 20417 1.  This submission includes reads tagged with the sequence CAGATC.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP016002,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2016 10 24|ENA LAST UPDATE:2018 11 16,20417_1#7.cram,cram,396397350.0,2642649.0,SC RUN 20417 1#7,0:75 1:75,A:103468605;C:95292253;G:94558692;T:103038245;N:39555,75,75,,,103468605,95292253,94558692,103038245,39555,ERX1776747,ERS1226813,ERA740537,European Nucleotide Archive,Wellcome Sanger Institute,2,0.96013,0.96276,0.17171,0.16938,0.72941,0.73046,0.54526,0.54527,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2016-06-28,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9825,ERR2102841,ERX2160152,ERS1883528,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N3 nabu RNA,SAMEA104224510,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224510|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N3 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N3 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N3 nabu RNA s,N3 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N3_R1_all.fastq.gz,fastq,1410139550.0,18670564.0,E MTAB 5992:N3 nabu RNA,0:75.53 1:0,A:353294009;C:340727934;G:322476371;T:393200193;N:441043,75,0,,,353294009,340727934,322476371,393200193,441043,ERX2160152,ERS1883528,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95434,,0.08906,,0.66935,,0.47788,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9826,ERR2102840,ERX2160151,ERS1883527,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N2 nabu RNA,SAMEA104224509,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224509|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N2 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N2 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N2 nabu RNA s,N2 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N2_R1_all.fastq.gz,fastq,1478621168.0,19576865.0,E MTAB 5992:N2 nabu RNA,0:75.53 1:0,A:369453299;C:359092235;G:341176884;T:408389810;N:508940,75,0,,,369453299,359092235,341176884,408389810,508940,ERX2160151,ERS1883527,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95582,,0.08202,,0.67718,,0.47812,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9827,ERR2102839,ERX2160150,ERS1883526,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N1 nabu RNA,SAMEA104224508,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224508|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N1 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N1 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N1 nabu RNA s,N1 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N1_R1_all.fastq.gz,fastq,1531713181.0,20277882.0,E MTAB 5992:N1 nabu RNA,0:75.54 1:0,A:386600603;C:373317031;G:350339456;T:420938891;N:517200,75,0,,,386600603,373317031,350339456,420938891,517200,ERX2160150,ERS1883526,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.9552,,0.08124,,0.67685,,0.47578,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9828,ERR2102838,ERX2160149,ERS1883525,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C3 control RNA,SAMEA104224507,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224507|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C3 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C3 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C3 control RNA s,C3 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C3_R1_all.fastq.gz,fastq,1380662008.0,18279108.0,E MTAB 5992:C3 control RNA,0:75.53 1:0,A:345997031;C:338444594;G:316575258;T:379195977;N:449148,75,0,,,345997031,338444594,316575258,379195977,449148,ERX2160149,ERS1883525,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95615,,0.08131,,0.68694,,0.45267,,74,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9829,ERR2102837,ERX2160148,ERS1883524,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C2 control RNA,SAMEA104224506,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224506|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C2 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C2 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C2 control RNA s,C2 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C2_R1_all.fastq.gz,fastq,1336640735.0,17695627.0,E MTAB 5992:C2 control RNA,0:75.54 1:0,A:338213530;C:326808990;G:303983789;T:367147896;N:486530,75,0,,,338213530,326808990,303983789,367147896,486530,ERX2160148,ERS1883524,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95427,,0.08628,,0.67706,,0.47245,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9830,ERR2102836,ERX2160147,ERS1883523,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C1 control RNA,SAMEA104224505,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224505|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C1 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C1 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C1 control RNA s,C1 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C1_R1_all.fastq.gz,fastq,1297694845.0,17180544.0,E MTAB 5992:C1 control RNA,0:75.53 1:0,A:322048172;C:316542683;G:299227724;T:359449433;N:426833,75,0,,,322048172,316542683,299227724,359449433,426833,ERX2160147,ERS1883523,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95505,,0.08541,,0.67659,,0.48159,,75,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10141,ERR4973564,ERX4792138,ERS5459722,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sibling 3,SAMEA7703213,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703213|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sibling 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 9899:sibling 3,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sibling 3 s,sibling 3 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,70_AACCGA_70_ACTAGC_S2_R1_001.fastq.gz,fastq,,,E MTAB 9899:sibling 3,0:76 1:0,A:385382600;C:210104151;G:238678838;T:315495923;N:5536,76,0,,,385382600,210104151,238678838,315495923,5536,ERX4792138,ERS5459722,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.82613,,0.13111,,0.77597,,0.53833,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10142,ERR4973563,ERX4792137,ERS5459721,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sibling 2,SAMEA7703212,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703212|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sibling 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 9899:sibling 2,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sibling 2 s,sibling 2 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,69_AGTTGA_69_CTTACA_S7_R1_001.fastq.gz,fastq,,,E MTAB 9899:sibling 2,0:76 1:0,A:405337161;C:226099266;G:255734601;T:341120121;N:5955,76,0,,,405337161,226099266,255734601,341120121,5955,ERX4792137,ERS5459721,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.84066,,0.12241,,0.77755,,0.56472,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10143,ERR4973562,ERX4792136,ERS5459720,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sibling 1,SAMEA7703211,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703211|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sibling 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 9899:sibling 1,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sibling 1 s,sibling 1 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,68_CCAATT_68_GTCCCG_S11_R1_001.fastq.gz,fastq,,,E MTAB 9899:sibling 1,0:76 1:0,A:440539801;C:236835299;G:268057277;T:355636994;N:6169,76,0,,,440539801,236835299,268057277,355636994,6169,ERX4792136,ERS5459720,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.82002,,0.12908,,0.77766,,0.54981,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10144,ERR4973561,ERX4792135,ERS5459719,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sfpq 3,SAMEA7703210,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703210|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sfpq 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:sfpq / |organism part:whole organism|sample name:E MTAB 9899:sfpq 3,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sfpq 3 s,sfpq 3 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:sfpq / ,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,67_TCGTTC_67_TGCTAT_S22_R1_001.fastq.gz,fastq,,,E MTAB 9899:sfpq 3,0:76 1:0,A:493165327;C:268347233;G:303443918;T:399152596;N:7138,76,0,,,493165327,268347233,303443918,399152596,7138,ERX4792135,ERS5459719,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.82521,,0.12349,,0.78545,,0.57446,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10145,ERR4973560,ERX4792134,ERS5459718,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sfpq 2,SAMEA7703209,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703209|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sfpq 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:sfpq / |organism part:whole organism|sample name:E MTAB 9899:sfpq 2,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sfpq 2 s,sfpq 2 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:sfpq / ,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,66_GACGAT_66_TCAGTC_S18_R1_001.fastq.gz,fastq,,,E MTAB 9899:sfpq 2,0:76 1:0,A:426637005;C:227027693;G:257342561;T:338159540;N:5909,76,0,,,426637005,227027693,257342561,338159540,5909,ERX4792134,ERS5459718,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.81933,,0.11571,,0.78593,,0.56675,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10146,ERR4973559,ERX4792133,ERS5459717,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sfpq 1,SAMEA7703208,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703208|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sfpq 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:sfpq / |organism part:whole organism|sample name:E MTAB 9899:sfpq 1,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sfpq 1 s,sfpq 1 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:sfpq / ,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,65_AAGCTC_65_AAGAAG_S3_R1_001.fastq.gz,fastq,,,E MTAB 9899:sfpq 1,0:76 1:0,A:425613638;C:225707961;G:254738302;T:336863560;N:5847,76,0,,,425613638,225707961,254738302,336863560,5847,ERX4792133,ERS5459717,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.81857,,0.11342,,0.78587,,0.56439,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11821,ERR11834690,ERX11232843,ERS16254762,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 4,SAMEA114265804,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265804|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 4|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250|organism part:whole organism|rin:9.6|sample name:E MTAB 13263:Sample 4|scientific name:Danio rerio|sex:na|stimulus:immunosuppression|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 4 p,Sample 4 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2113_dre_C1_clobetasolpropionate_lib667285_10169_3_2.fastq.gz NG-32417_R2113_dre_C1_clobetasolpropionate_lib667285_10169_3_1.fastq.gz,fastq fastq,9764006696.0,32331148.0,E MTAB 13263:NG 32417 R2113 dre C1 clobetasolpropionate lib667285 10169 3 ,0:151 1:151,A:2627275848;C:2223323771;G:2323190525;T:2590103027;N:113525,151,151,,,2627275848,2223323771,2323190525,2590103027,113525,ERX11232843,ERS16254762,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95424,0.95502,0.12596,0.12401,0.65884,0.65825,0.48134,0.48327,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11822,ERR11834689,ERX11232842,ERS16254761,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 3,SAMEA114265803,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265803|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 3|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:0|organism part:whole organism|rin:9.4|sample name:E MTAB 13263:Sample 3|scientific name:Danio rerio|sex:na|stimulus:n1|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 3 p,Sample 3 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2112_dre_nc_clobetasolpropionate_lib673071_10180_1_2.fastq.gz NG-32417_R2112_dre_nc_clobetasolpropionate_lib673071_10180_1_1.fastq.gz,fastq fastq,13326663550.0,44128025.0,E MTAB 13263:NG 32417 R2112 dre nc clobetasolpropionate lib673071 10180 1 ,0:151 1:151,A:3641640344;C:3020489123;G:3072643196;T:3591659412;N:231475,151,151,,,3641640344,3020489123,3072643196,3591659412,231475,ERX11232842,ERS16254761,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95271,0.95293,0.11945,0.1151,0.65819,0.6579,0.47257,0.47803,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11823,ERR11834684,ERX11232837,ERS16254756,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 1,SAMEA114265798,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265798|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 1|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:0|organism part:whole organism|rin:9.3|sample name:E MTAB 13263:Sample 1|scientific name:Danio rerio|sex:na|stimulus:n1|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 1 p,Sample 1 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2110_dre_nc_clobetasolpropionate_lib667282_10169_3_1.fastq.gz NG-32417_R2110_dre_nc_clobetasolpropionate_lib667282_10169_3_2.fastq.gz,fastq fastq,10152616370.0,33617935.0,E MTAB 13263:NG 32417 R2110 dre nc clobetasolpropionate lib667282 10169 3 ,0:151 1:151,A:2743478864;C:2319134955;G:2378048842;T:2711839167;N:114542,151,151,,,2743478864,2319134955,2378048842,2711839167,114542,ERX11232837,ERS16254756,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95273,0.95457,0.13567,0.13174,0.65896,0.65841,0.47947,0.47815,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11824,ERR11834691,ERX11232844,ERS16254763,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 5,SAMEA114265805,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265805|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 5|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250|organism part:whole organism|rin:9.2|sample name:E MTAB 13263:Sample 5|scientific name:Danio rerio|sex:na|stimulus:immunosuppression|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 5 p,Sample 5 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2114_dre_C1_clobetasolpropionate_lib667286_10169_3_1.fastq.gz NG-32417_R2114_dre_C1_clobetasolpropionate_lib667286_10169_3_2.fastq.gz,fastq fastq,11690304334.0,38709617.0,E MTAB 13263:NG 32417 R2114 dre C1 clobetasolpropionate lib667286 10169 3 ,0:151 1:151,A:3142106866;C:2677986743;G:2767050957;T:3103028799;N:130969,151,151,,,3142106866,2677986743,2767050957,3103028799,130969,ERX11232844,ERS16254763,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95418,0.95523,0.12548,0.12397,0.66026,0.66016,0.46767,0.47253,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11825,ERR11834688,ERX11232841,ERS16254760,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 2,SAMEA114265802,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265802|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 2|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:0|organism part:whole organism|rin:9.6|sample name:E MTAB 13263:Sample 2|scientific name:Danio rerio|sex:na|stimulus:n1|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 2 p,Sample 2 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2111_dre_nc_clobetasolpropionate_lib673070_10180_1_1.fastq.gz NG-32417_R2111_dre_nc_clobetasolpropionate_lib673070_10180_1_2.fastq.gz,fastq fastq,11827163184.0,39162792.0,E MTAB 13263:NG 32417 R2111 dre nc clobetasolpropionate lib673070 10180 1 ,0:151 1:151,A:3256286612;C:2657918302;G:2701905502;T:3210846546;N:206222,151,151,,,3256286612,2657918302,2701905502,3210846546,206222,ERX11232841,ERS16254760,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95203,0.95292,0.12277,0.11772,0.66048,0.65837,0.47243,0.4729,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11826,ERR11834693,ERX11232846,ERS16254765,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 7,SAMEA114265807,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265807|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 7|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:4000|organism part:whole organism|rin:9.7|sample name:E MTAB 13263:Sample 7|scientific name:Danio rerio|sex:na|stimulus:immunostimulation|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 7 p,Sample 7 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2116_dre_nc_imq_clobetasolpropionate_lib667288_10169_3_1.fastq.gz NG-32417_R2116_dre_nc_imq_clobetasolpropionate_lib667288_10169_3_2.fastq.gz,fastq fastq,11114382784.0,36802592.0,E MTAB 13263:NG 32417 R2116 dre nc imq clobetasolpropionate lib667288 10169 3 ,0:151 1:151,A:2997376944;C:2547742011;G:2613273908;T:2955864850;N:125071,151,151,,,2997376944,2547742011,2613273908,2955864850,125071,ERX11232846,ERS16254765,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95392,0.9539,0.12951,0.12707,0.65628,0.65731,0.48132,0.48179,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11827,ERR11834695,ERX11232848,ERS16254767,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 9,SAMEA114265809,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265809|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 9|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:4000|organism part:whole organism|rin:9.9|sample name:E MTAB 13263:Sample 9|scientific name:Danio rerio|sex:na|stimulus:immunostimulation|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 9 p,Sample 9 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2118_dre_nc_imq_clobetasolpropionate_lib667290_10169_3_1.fastq.gz NG-32417_R2118_dre_nc_imq_clobetasolpropionate_lib667290_10169_3_2.fastq.gz,fastq fastq,9422294300.0,31199650.0,E MTAB 13263:NG 32417 R2118 dre nc imq clobetasolpropionate lib667290 10169 3 ,0:151 1:151,A:2541445212;C:2157798531;G:2214381344;T:2508560588;N:108625,151,151,,,2541445212,2157798531,2214381344,2508560588,108625,ERX11232848,ERS16254767,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95337,0.95433,0.13046,0.12718,0.65845,0.65815,0.48198,0.48414,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11828,ERR11834687,ERX11232840,ERS16254759,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 12,SAMEA114265801,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265801|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 12|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250 CP + 4000 IMQ|organism part:whole organism|rin:9.7|sample name:E MTAB 13263:Sample 12|scientific name:Danio rerio|sex:na|stimulus:immunosuppression and immunostimulation|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 12 p,Sample 12 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2121_dre_C1_imq_clobetasolpropionate_lib667293_10169_3_2.fastq.gz NG-32417_R2121_dre_C1_imq_clobetasolpropionate_lib667293_10169_3_1.fastq.gz,fastq fastq,9285032280.0,30745140.0,E MTAB 13263:NG 32417 R2121 dre C1 imq clobetasolpropionate lib667293 10169 3 ,0:151 1:151,A:2504765552;C:2110325477;G:2196928032;T:2472905759;N:107460,151,151,,,2504765552,2110325477,2196928032,2472905759,107460,ERX11232840,ERS16254759,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95411,0.95451,0.12502,0.12228,0.65829,0.65774,0.48259,0.47946,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11829,ERR11834694,ERX11232847,ERS16254766,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 8,SAMEA114265808,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265808|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 8|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:4000|organism part:whole organism|rin:9.5|sample name:E MTAB 13263:Sample 8|scientific name:Danio rerio|sex:na|stimulus:immunostimulation|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 8 p,Sample 8 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2117_dre_nc_imq_clobetasolpropionate_lib667289_10169_3_1.fastq.gz NG-32417_R2117_dre_nc_imq_clobetasolpropionate_lib667289_10169_3_2.fastq.gz,fastq fastq,10247527118.0,33932209.0,E MTAB 13263:NG 32417 R2117 dre nc imq clobetasolpropionate lib667289 10169 3 ,0:151 1:151,A:2766675319;C:2342307825;G:2405294253;T:2733131648;N:118073,151,151,,,2766675319,2342307825,2405294253,2733131648,118073,ERX11232847,ERS16254766,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.9541,0.95434,0.13364,0.13098,0.6576,0.6565,0.48068,0.48029,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11830,ERR11834692,ERX11232845,ERS16254764,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 6,SAMEA114265806,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265806|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 6|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250|organism part:whole organism|rin:10|sample name:E MTAB 13263:Sample 6|scientific name:Danio rerio|sex:na|stimulus:immunosuppression|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 6 p,Sample 6 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2115_dre_C1_clobetasolpropionate_lib667287_10169_3_1.fastq.gz NG-32417_R2115_dre_C1_clobetasolpropionate_lib667287_10169_3_2.fastq.gz,fastq fastq,10440673634.0,34571767.0,E MTAB 13263:NG 32417 R2115 dre C1 clobetasolpropionate lib667287 10169 3 ,0:151 1:151,A:2805459166;C:2397120759;G:2463616298;T:2774359989;N:117422,151,151,,,2805459166,2397120759,2463616298,2774359989,117422,ERX11232845,ERS16254764,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95568,0.9548,0.13056,0.12563,0.65882,0.66332,0.49162,0.48586,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11831,ERR11834685,ERX11232838,ERS16254757,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 10,SAMEA114265799,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265799|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 10|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250 CP + 4000 IMQ|organism part:whole organism|rin:9.4|sample name:E MTAB 13263:Sample 10|scientific name:Danio rerio|sex:na|stimulus:immunosuppression and immunostimulation|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 10 p,Sample 10 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2119_dre_C1_imq_clobetasolpropionate_lib667291_10169_3_2.fastq.gz NG-32417_R2119_dre_C1_imq_clobetasolpropionate_lib667291_10169_3_1.fastq.gz,fastq fastq,11267068246.0,37308173.0,E MTAB 13263:NG 32417 R2119 dre C1 imq clobetasolpropionate lib667291 10169 3 ,0:151 1:151,A:3042432765;C:2574394239;G:2642086000;T:3008026288;N:128954,151,151,,,3042432765,2574394239,2642086000,3008026288,128954,ERX11232838,ERS16254757,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.95345,0.95411,0.13324,0.13062,0.65796,0.65892,0.48176,0.48174,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
11832,ERR11834686,ERX11232839,ERS16254758,ERP150242,PRJEB65099,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E-MTAB-13263,Transcriptome Analysis,Within the regulatory framework on the approval of new substances  the assessment of immunotoxic modes of action MoA is currently not covered. This is not least due to the lack of standardized methods and reliable validated biomarkers for immunotoxic effects. The experimental set up was designed to analyze the compound specific response of zebrafish embryos to two immunomodulative reference substances  clobetasol propionate CP  CAS 25122 46 7 and imiquimod IMQ  CAS 99011 02 6  on the global level of gene expression. The obtained results were used to i identify potential biomarker candidates for the assessment of immunotoxic MoAs  ii identify compound specific molecular signatures  iii evaluate the reliability of data acquisition using OMICs coupled approaches and iv to assess the suitability of the zebrafish embryo as an alternative model for the human representative investigation of psoriatic effects. For this  the transcriptomic profiles of embryos were bioinformatically analysed subsequent to an CP induced immunosuppression in absence or presence of an IMQ induced immune challenge  i.e. the simulation of a resting and an activated immune system.   In a modified version of the zebrafish embryo toxicity test OECD 236  15 fertilized eggs were exposed to either CP 250 nM or to IMQ 4000 nM or to a combination of both under semi static conditions. Exposure to CP started at 2 hpf until 72 hpf. Exposure to IMQ started at 48 hpf until 72 hpf. Untreated embryos reared in medium without xxx nor IMQ dissolved was used as a negative control. All conditions comprised three biological replicates. Medium was exchanged on a daily basis by renewing half its volume. Occurrence of morphological changes and indicators of lethality as described in the OECD test guideline 236 were examined microscopically on a daily basis. At 72 hpf  all larvae were pooled for each sample for RNA extraction using a NucleoSpin RNA/Protein kit Macherey Nagel following the manufacturer's protocol. 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 NovaSeq 6000 System Illumina in 150 bp paired end mode  producing a minimum of 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the Danio 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:2023 12 01|ENA LAST UPDATE:2023 12 01,,Protocols: At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos. 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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol” Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions. The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution. RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice. High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,Sample 11,SAMEA114265800,"Department Ecotoxicogenomics, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany",ENA FIRST PUBLIC:2023 12 01T00:42:51Z|ENA LAST UPDATE:2023 12 01T00:42:51Z|External Id:SAMEA114265800|INSDC center name:Department Ecotoxicogenomics  Fraunhofer Institute for Molecular Biology and Applied Ecology IME  Schmallenberg  Germany|INSDC first public:2023 12 01T00:42:51Z|INSDC last update:2023 12 01T00:42:51Z|INSDC status:public|Submitter Id:E MTAB 13263:Sample 11|age:3|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|genotype:AB|geographic location country and/or sea:not collected|isolate:not applicable|nominal concentration in medium:250 CP + 4000 IMQ|organism part:whole organism|rin:10|sample name:E MTAB 13263:Sample 11|scientific name:Danio rerio|sex:na|stimulus:immunosuppression and immunostimulation|strain:Wildtype AB,,,,,,,,,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,E MTAB 13263:Sample 11 p,Sample 11 p,Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,At 72 hpf  for each sample  all 15 zebrafish embryos were picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Excessive liquid was removed and tubes were placed on ice to euthanize the embryos.   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: All experiments were performed using zebrafish Danio rerio embryos of the wild type strain AB. Adult fish were originally obtained from West Aquarium GmbH  Germany  and were kept in 150 l tanks under flow through conditions at 26 ± 2 °C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME  Schmallenberg  Germany. TetraMin® Tetra Werke  Germany was used as daily main feed  regularly supplemented with nauplii of Artemia salina. Fish were constantly bred for several generations without xxx between tanks  making the embryos deriving from different spawning groups tanks independent biological replicates. For egg collection  glass spawning trays equipped with whirled cords of green glass pearls to stimulate spawning and covered with wired mesh to prevent cannibalism were put into the tanks the day before tests were started OECD  2013. The morning post  eggs were collected from the trays using a sieve  rinsed with pre tempered system water to remove remaining feces  gathered in glass jars filled with pre tempered aerated system water and stored at a controlled temperature of 26 ± 1 °C until further use.  Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. For details on the treatment see “treatment protocol”   Clobetasol propionate 21 Chlor 9 fluor 11β 17 dihydroxy 16β methylpregna 1 4 dien 3 20 dion 17 propionat  purity ≥ 98 %  CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine  purity ≥ 95 %  CAS no. 9901 02 6 were purchased from BIOMOL GmbH  Hamburg  Germany. For IMQ  a stock solution in acetone with a nominal concentration of 0.1 mg/ml was prepared. For CP  a stock solution in dimethyl sulfoxide DMSO with a nominal concentration of 2.5 mM was prepared. To obtain a test solution with a nominal concentration of 4666 nM IMQ  2242.5 µl of the IMQ stock solution was added to a glass bottle. To equalize the amount of added acetone amongst all solutions  equal volume of pure acetone without xxx was added to glass bottles for all remaining test solutions. For all test solutions containing 250 nM CP  20 µl of the CP stock solution was added to the glass bottles post complete evaporation of the acetone and filled with copper reduced tap water in the following referred to as cu red water to a final volume of 200 ml. Test solutions without xxx were prepared alike adding 20 µl DMSO without xxx. All solutions were sonicated for 30 min at room temperature Sonorex RK 100H  Bandelin  Germany. Final solutions were thus cu red water with 0.01 % DMSO  4666 nM IMQ in cu red water with 0.01 % DMSO  250 nM CP in cu red water with 0.01 % DMSO and 4666 nM IMQ plus 250 nM CP in cu red water with 0.01 % DMSO. Due to a mandatory dilution during the methodological procedure a nominal working concentration of 4000 nM was achieved for IMQ in these solutions.  The test solutions were freshly prepared one day prior the start of the experiment and stored at room temperature in the dark. They were constantly aerated and used over the course of the 72 hours exposure experiment. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment.  In order to minimize the differences between replicates and conditions in exposure durations  the selection of embryos was performed in two steps: at 2 hpf  approx. 50 embryos from spawning batches with a minimum fertilization rate ≥ 90 % were transferred to previously overnight saturated glass petri dishes 6 cm diameter refilled with 7 ml of the corresponding test solutions for each replicate and condition. Embryos of the control and the IMQ condition were thus transferred to medium without xxx compound  embryos of the CP and combined CP+IMQ condition were transferred to medium supplemented with 250 nM CP. Once in solution  15 healthy and fertilized embryos  indicated by a well shaped blastodisc between the 128 cell and 1k cell stage of development were selected per replicate and condition for experiments. Embryos were incubated at a controlled temperature of 26 ± 1°C and a 14:10 h light/dark cycle artificially created with tubular fluorescent lamps with the lights switched on at 8 am. Medium was refreshed at 24 hpf by renewing half its volume. Embryos were inspected microscopically on a daily basis and at the end of the experiment using an OZL 451 stereomicroscope KERN & Sohn  Germany in order to monitor the occurrence of indicators of lethality as defined by the OECD FET test guideline  namely coagulation  lack of somite formation  lack of a heartbeat  non detachment of the tail OECD  2013 as well as further indicators of malformations such as scoliosis  formation of edema or lack of pigmentation. At 47 hpf  embryos were manually dechorionated using two pointy forceps. At 48 hpf  the immune challenge was started by transferring the embryos of the IMQ condition and the combined CP+IMQ condition to the respective test solution supplemented with IMQ. For this and in order to equalized the subsequent dilution of media between replicates and conditions  embryos were gathered in 1 ml of the aged medium and transferred with this volume into newly saturated glass dishes  filled with 6 ml of the corresponding fresh medium. Due to this dilution  a nominal working concentration of 4000 nM IMQ was achieved for the immune challenge. Embryos of the control condition and the CP condition were handled alike but without xxx the type of test solution.  RNA was extracted using a NucleoSpin RNA/Protein kit Macherey Nagel  Düren  Germany. Briefly  frozen embryos were transferred to screw cap tubes filled with 350 µl kit specific lysis buffer RP1 buffer and Lysing Matrix D ceramic beads MP Biomedicals  Irvine  USA and homogenized using a FastPrep 24 MP Biomedicals  Irvine  USA device at 5 m/s for 1 min. RP1 buffer was freshly prepared with TCEP as reducing agent prior extraction. Further steps were performed following the manufacturer's extraction protocol. As quality measures  purity and concentration of extracted RNA were determined using a NanoDrop 2000 device Thermo Scientific  Waltham  USA and RNA integrity numbers RIN were determined using a Bioanalyzer 2100 device Agilent  Santa Clara  USA with samples prepared using a RNA Pico 6000 kit Agilent  Santa Clara  USA following the manufacturer's instructions. Only samples with a RIN > 9 were used for downstream analysis. Samples were stored at  80°C until they were send to the sequencing facility on dry ice.  High quality RNA samples with RIN > 9 were selected for RNA seq library preparation and sequencing  performed by Eurofins Genomics Germany GmbH  Ebersberg  Germany. Briefly  Poly A containing protein coding mRNA molecules were purified from total RNA  randomly fragmentated and subjected to random primed strand specific cDNA library preparation using the TruSeq RNA library Prep Kit v2 Illumina following the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP150242,Illumina NovaSeq 6000 paired end sequencing; Transcriptomic profiling of  TLR 7 mediated immune challenge in zebrafish embryos in the presence and absence of glucocorticoid induced immunosuppression,ENA FIRST PUBLIC:2023 12 01|ENA LAST UPDATE:2023 12 01,NG-32417_R2120_dre_C1_imq_clobetasolpropionate_lib667292_10169_3_2.fastq.gz NG-32417_R2120_dre_C1_imq_clobetasolpropionate_lib667292_10169_3_1.fastq.gz,fastq fastq,9922486330.0,32855915.0,E MTAB 13263:NG 32417 R2120 dre C1 imq clobetasolpropionate lib667292 10169 3 ,0:151 1:151,A:2673462020;C:2268840894;G:2345658284;T:2634411815;N:113317,151,151,,,2673462020,2268840894,2345658284,2634411815,113317,ERX11232839,ERS16254758,ERA26742386,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.9551,0.95621,0.1193,0.11675,0.65833,0.65827,0.48596,0.48547,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2023-12-01,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29053,SRR26990806,SRX22683813,SRS19677527,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,zebrafish itgavko tc 8d 3,GSM7924146,,source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf|geo loc name:missing|collection date:missing,zebrafish itgavko tc 8d 3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,whole fish with tailfin cut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf,GSM7924146,GSM7924146: zebrafish itgavko tc 8d 3; Danio rerio; RNA Seq,GSM7924146 r1,GSM7924146,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,6_zebrafish_itgavko_tc_8d_3_S31_L001_R2_001.fastq.gz 6_zebrafish_itgavko_tc_8d_3_S31_L001_R1_001.fastq.gz,fastq fastq,3875161320.0,12831660.0,GSM7924146 r1,0:151 1:151,A:1223303253;C:711567515;G:746979670;T:1193309732;N:1150,151,151,,,1223303253,711567515,746979670,1193309732,1150,SRX22683813,SRS19677527,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.84595,0.84551,0.30568,0.30506,0.77329,0.76948,0.63885,0.64046,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29054,SRR26990807,SRX22683812,SRS19677526,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,zebrafish itgavko tc 8d 2,GSM7924145,,source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf|geo loc name:missing|collection date:missing,zebrafish itgavko tc 8d 2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,whole fish with tailfin cut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf,GSM7924145,GSM7924145: zebrafish itgavko tc 8d 2; Danio rerio; RNA Seq,GSM7924145 r1,GSM7924145,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,5_zebrafish_itgavko_tc_8d_2_S30_L001_R1_001.fastq.gz 5_zebrafish_itgavko_tc_8d_2_S30_L001_R2_001.fastq.gz,fastq fastq,4365991652.0,14456926.0,GSM7924145 r1,0:151 1:151,A:1270600077;C:909032449;G:940039197;T:1246318704;N:1225,151,151,,,1270600077,909032449,940039197,1246318704,1225,SRX22683812,SRS19677526,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.91871,0.91856,0.21085,0.20755,0.71114,0.70873,0.45669,0.45984,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29055,SRR26990808,SRX22683811,SRS19677525,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,zebrafish itgavko tc 8d 1,GSM7924144,,source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf|geo loc name:missing|collection date:missing,zebrafish itgavko tc 8d 1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,whole fish with tailfin cut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:whole fish with tailfin cut|genotype:itgavKO mutant|time:8dpf,GSM7924144,GSM7924144: zebrafish itgavko tc 8d 1; Danio rerio; RNA Seq,GSM7924144 r1,GSM7924144,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,4_zebrafish_itgavko_tc_8d_1_S29_L001_R1_001.fastq.gz 4_zebrafish_itgavko_tc_8d_1_S29_L001_R2_001.fastq.gz,fastq fastq,4802635634.0,15902767.0,GSM7924144 r1,0:151 1:151,A:1431003343;C:965403922;G:1003504713;T:1402722287;N:1369,151,151,,,1431003343,965403922,1003504713,1402722287,1369,SRX22683811,SRS19677525,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.90555,0.90464,0.24806,0.24593,0.72182,0.72007,0.46914,0.47508,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29056,SRR26990809,SRX22683810,SRS19677524,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,zebrafish wt tc 8d 3,GSM7924143,,source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf|geo loc name:missing|collection date:missing,zebrafish wt tc 8d 3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,whole fish with tailfin cut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf,GSM7924143,GSM7924143: zebrafish wt tc 8d 3; Danio rerio; RNA Seq,GSM7924143 r1,GSM7924143,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,3_zebrafish_wt_tc_8d_3_S28_L001_R1_001.fastq.gz 3_zebrafish_wt_tc_8d_3_S28_L001_R2_001.fastq.gz,fastq fastq,4510890648.0,14936724.0,GSM7924143 r1,0:151 1:151,A:1375725383;C:876879135;G:915216593;T:1343068155;N:1382,151,151,,,1375725383,876879135,915216593,1343068155,1382,SRX22683810,SRS19677524,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.87519,0.87203,0.27672,0.27432,0.74282,0.74054,0.54199,0.54873,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29057,SRR26990810,SRX22683809,SRS19677523,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,zebrafish wt tc 8d 2,GSM7924142,,source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf|geo loc name:missing|collection date:missing,zebrafish wt tc 8d 2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,whole fish with tailfin cut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf,GSM7924142,GSM7924142: zebrafish wt tc 8d 2; Danio rerio; RNA Seq,GSM7924142 r1,GSM7924142,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,2_zebrafish_wt_tc_8d_2_S27_L001_R1_001.fastq.gz 2_zebrafish_wt_tc_8d_2_S27_L001_R2_001.fastq.gz,fastq fastq,4596331280.0,15219640.0,GSM7924142 r1,0:151 1:151,A:1337992161;C:955572266;G:991264463;T:1311501025;N:1365,151,151,,,1337992161,955572266,991264463,1311501025,1365,SRX22683809,SRS19677523,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.91445,0.91384,0.21247,0.20919,0.71135,0.70893,0.46349,0.47487,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29058,SRR26990811,SRX22683808,SRS19677522,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation  brain abnormalities  and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation  atopy  and colitis  and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies  we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore  knockout itgav  /  zebrafish embryos developed brain defects with loss of microglia and juvenile itgav  /  zebrafish developed colitis. Together  we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line  and itgav /  line  at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,zebrafish wt tc 8d 1,GSM7924141,,source name:whole fish with tailfin cut|tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf|geo loc name:missing|collection date:missing,zebrafish wt tc 8d 1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts.  Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,whole fish with tailfin cut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav  /  mutants were pooled n=15  repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf  embryos were obtained via natural mating and cultured in embryo E3 buffer  raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C.  For wt and itgav KO mutants at 50dpf  embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:whole fish with tailfin cut|genotype:wildtype|time:8dpf,GSM7924141,GSM7924141: zebrafish wt tc 8d 1; Danio rerio; RNA Seq,GSM7924141 r1,GSM7924141,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched  rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,1_zebrafish_wt_tc_8d_1_S26_L001_R2_001.fastq.gz 1_zebrafish_wt_tc_8d_1_S26_L001_R1_001.fastq.gz,fastq fastq,3796122786.0,12569943.0,GSM7924141 r1,0:151 1:151,A:1127981217;C:766135618;G:796849753;T:1105155152;N:1046,151,151,,,1127981217,766135618,796849753,1105155152,1046,SRX22683808,SRS19677522,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.9074,0.90541,0.24401,0.24217,0.7205,0.7176,0.46736,0.47258,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29125,SRR32025056,SRX27375433,SRS23810897,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,smad6ab DKO 5  biol rep 1  5 dpf  5 fish pooled,GSM8741296,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad6a/b DKO|geo loc name:missing|collection date:missing,smad6ab DKO 5  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:smad6a/b DKO,GSM8741296,GSM8741296: smad6ab DKO 5  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741296 r1,GSM8741296,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,30_smad6a__smad6b__F11_R1.fastq.gz,fastq,1783531650.0,23780422.0,GSM8741296 r1,0:75,A:612499747;C:307171870;G:341630182;T:521913046;N:316805,75,,,,612499747,307171870,341630182,521913046,316805,SRX27375433,SRS23810897,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29126,SRR32025057,SRX27375432,SRS23810896,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,smad6ab DKO 4  biol rep 1  5 dpf  5 fish pooled,GSM8741295,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad6a/b DKO|geo loc name:missing|collection date:missing,smad6ab DKO 4  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:smad6a/b DKO,GSM8741295,GSM8741295: smad6ab DKO 4  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741295 r1,GSM8741295,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,29_smad6a__smad6b__E11_R1.fastq.gz,fastq,1806895725.0,24091943.0,GSM8741295 r1,0:75,A:610799963;C:310255661;G:349091544;T:536431072;N:317485,75,,,,610799963,310255661,349091544,536431072,317485,SRX27375432,SRS23810896,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29127,SRR32025058,SRX27375431,SRS23810895,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,smad6ab DKO 3  biol rep 1  5 dpf  5 fish pooled,GSM8741294,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad6a/b DKO|geo loc name:missing|collection date:missing,smad6ab DKO 3  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:smad6a/b DKO,GSM8741294,GSM8741294: smad6ab DKO 3  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741294 r1,GSM8741294,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,28_smad6a__smad6b__D11_R1.fastq.gz,fastq,1236162375.0,16482165.0,GSM8741294 r1,0:75,A:417424019;C:209354549;G:238058828;T:371172361;N:152618,75,,,,417424019,209354549,238058828,371172361,152618,SRX27375431,SRS23810895,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29128,SRR32025059,SRX27375430,SRS23810893,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,smad6ab DKO 2  biol rep 1  5 dpf  5 fish pooled,GSM8741293,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad6a/b DKO|geo loc name:missing|collection date:missing,smad6ab DKO 2  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:smad6a/b DKO,GSM8741293,GSM8741293: smad6ab DKO 2  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741293 r1,GSM8741293,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,27_smad6a__smad6b__C11_R1.fastq.gz,fastq,1239721050.0,16529614.0,GSM8741293 r1,0:75,A:422806413;C:210247744;G:238495376;T:367964420;N:207097,75,,,,422806413,210247744,238495376,367964420,207097,SRX27375430,SRS23810893,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29129,SRR32025060,SRX27375429,SRS23810894,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,smad6ab DKO 1  biol rep 1  5 dpf  5 fish pooled,GSM8741292,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad6a/b DKO|geo loc name:missing|collection date:missing,smad6ab DKO 1  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:smad6a/b DKO,GSM8741292,GSM8741292: smad6ab DKO 1  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741292 r1,GSM8741292,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,26_smad6a__smad6b__B11_R1.fastq.gz,fastq,1771498800.0,23619984.0,GSM8741292 r1,0:75,A:600616051;C:303681611;G:340472236;T:526419468;N:309434,75,,,,600616051,303681611,340472236,526419468,309434,SRX27375429,SRS23810894,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29130,SRR32025061,SRX27375428,SRS23810892,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 5 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741291,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:wt control|geo loc name:missing|collection date:missing,control 5 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,GSM8741291,GSM8741291: control 5 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741291 r1,GSM8741291,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,25_wt_control_A11_R1.fastq.gz,fastq,1574255025.0,20990067.0,GSM8741291 r1,0:75,A:544358067;C:268587913;G:299883067;T:461155939;N:270039,75,,,,544358067,268587913,299883067,461155939,270039,SRX27375428,SRS23810892,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29131,SRR32025062,SRX27375427,SRS23810891,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 4 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741290,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:wt control|geo loc name:missing|collection date:missing,control 4 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,GSM8741290,GSM8741290: control 4 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741290 r1,GSM8741290,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,24_wt_control_H10_R1.fastq.gz,fastq,1197613800.0,15968184.0,GSM8741290 r1,0:75,A:413692477;C:202818991;G:227848971;T:353083087;N:170274,75,,,,413692477,202818991,227848971,353083087,170274,SRX27375427,SRS23810891,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29132,SRR32025063,SRX27375426,SRS23810890,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 3 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741289,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:wt control|geo loc name:missing|collection date:missing,control 3 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,GSM8741289,GSM8741289: control 3 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741289 r1,GSM8741289,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,23_wt_control_G10_R1.fastq.gz,fastq,1433154750.0,19108730.0,GSM8741289 r1,0:75,A:493379384;C:244908245;G:274361129;T:420258548;N:247444,75,,,,493379384,244908245,274361129,420258548,247444,SRX27375426,SRS23810890,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29133,SRR32025064,SRX27375425,SRS23810888,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 2 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741288,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:wt control|geo loc name:missing|collection date:missing,control 2 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,GSM8741288,GSM8741288: control 2 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741288 r1,GSM8741288,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,22_wt_control_F10_R1.fastq.gz,fastq,1283795850.0,17117278.0,GSM8741288 r1,0:75,A:442456808;C:219464610;G:244269392;T:377385874;N:219166,75,,,,442456808,219464610,244269392,377385874,219166,SRX27375425,SRS23810888,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29134,SRR32025065,SRX27375424,SRS23810889,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 1 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741287,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:wt control|geo loc name:missing|collection date:missing,control 1 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,GSM8741287,GSM8741287: control 1 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741287 r1,GSM8741287,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,21_wt_control_E10_R1.fastq.gz,fastq,1620787500.0,21610500.0,GSM8741287 r1,0:75,A:556979571;C:275622807;G:309210789;T:478725788;N:248545,75,,,,556979571,275622807,309210789,478725788,248545,SRX27375424,SRS23810889,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29135,SRR32025066,SRX27375423,SRS23810887,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,smad3ab DKO 5  biol rep 1  5 dpf  5 fish pooled,GSM8741286,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad3a/b DKO|geo loc name:missing|collection date:missing,smad3ab DKO 5  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:smad3a/b DKO,GSM8741286,GSM8741286: smad3ab DKO 5  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741286 r1,GSM8741286,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,20_smad3a__smad3b__D10_R1.fastq.gz,fastq,1664067900.0,22187572.0,GSM8741286 r1,0:75,A:575504153;C:284148304;G:316755855;T:487400701;N:258887,75,,,,575504153,284148304,316755855,487400701,258887,SRX27375423,SRS23810887,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29136,SRR32025067,SRX27375422,SRS23810886,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,smad3ab DKO 4  biol rep 1  5 dpf  5 fish pooled,GSM8741285,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad3a/b DKO|geo loc name:missing|collection date:missing,smad3ab DKO 4  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:smad3a/b DKO,GSM8741285,GSM8741285: smad3ab DKO 4  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741285 r1,GSM8741285,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,19_smad3a__smad3b__C10_R1.fastq.gz,fastq,1277250825.0,17030011.0,GSM8741285 r1,0:75,A:441711745;C:218346228;G:242350714;T:374666966;N:175172,75,,,,441711745,218346228,242350714,374666966,175172,SRX27375422,SRS23810886,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29137,SRR32025068,SRX27375421,SRS23810885,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,smad3ab DKO 3  biol rep 1  5 dpf  5 fish pooled,GSM8741284,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad3a/b DKO|geo loc name:missing|collection date:missing,smad3ab DKO 3  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:smad3a/b DKO,GSM8741284,GSM8741284: smad3ab DKO 3  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741284 r1,GSM8741284,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,18_smad3a__smad3b__B10_R1.fastq.gz,fastq,1564334850.0,20857798.0,GSM8741284 r1,0:75,A:538189348;C:271673806;G:298029553;T:456167924;N:274219,75,,,,538189348,271673806,298029553,456167924,274219,SRX27375421,SRS23810885,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29138,SRR32025069,SRX27375420,SRS23810883,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,smad3ab DKO 2  biol rep 1  5 dpf  5 fish pooled,GSM8741283,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad3a/b DKO|geo loc name:missing|collection date:missing,smad3ab DKO 2  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:smad3a/b DKO,GSM8741283,GSM8741283: smad3ab DKO 2  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741283 r1,GSM8741283,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,17_smad3a__smad3b__A10_R1.fastq.gz,fastq,1496334900.0,19951132.0,GSM8741283 r1,0:75,A:514961004;C:254586630;G:285562274;T:440963052;N:261940,75,,,,514961004,254586630,285562274,440963052,261940,SRX27375420,SRS23810883,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29139,SRR32025070,SRX27375419,SRS23810884,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,smad3ab DKO 1  biol rep 1  5 dpf  5 fish pooled,GSM8741282,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad3a/b DKO|geo loc name:missing|collection date:missing,smad3ab DKO 1  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:smad3a/b DKO,GSM8741282,GSM8741282: smad3ab DKO 1  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741282 r1,GSM8741282,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,16_smad3a__smad3b__H9_R1.fastq.gz,fastq,1403963250.0,18719510.0,GSM8741282 r1,0:75,A:488946191;C:233615962;G:269240931;T:411958629;N:201537,75,,,,488946191,233615962,269240931,411958629,201537,SRX27375419,SRS23810884,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29140,SRR32025071,SRX27375418,SRS23810882,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 5 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741281,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:wt control|geo loc name:missing|collection date:missing,control 5 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,GSM8741281,GSM8741281: control 5 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741281 r1,GSM8741281,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,15_wt_control_G9_R1.fastq.gz,fastq,1565513400.0,20873512.0,GSM8741281 r1,0:75,A:537915091;C:264328012;G:304123957;T:458903666;N:242674,75,,,,537915091,264328012,304123957,458903666,242674,SRX27375418,SRS23810882,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29141,SRR32025072,SRX27375417,SRS23810881,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 4 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741280,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:wt control|geo loc name:missing|collection date:missing,control 4 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,GSM8741280,GSM8741280: control 4 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741280 r1,GSM8741280,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,14_wt_control_F9_R1.fastq.gz,fastq,1289377350.0,17191698.0,GSM8741280 r1,0:75,A:444884871;C:212056955;G:249450087;T:382793805;N:191632,75,,,,444884871,212056955,249450087,382793805,191632,SRX27375417,SRS23810881,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29142,SRR32025073,SRX27375416,SRS23810880,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 3 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741279,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:wt control|geo loc name:missing|collection date:missing,control 3 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,GSM8741279,GSM8741279: control 3 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741279 r1,GSM8741279,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,13_wt_control_E9_R1.fastq.gz,fastq,1500149700.0,20001996.0,GSM8741279 r1,0:75,A:516842151;C:249094684;G:289026249;T:444994403;N:192213,75,,,,516842151,249094684,289026249,444994403,192213,SRX27375416,SRS23810880,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29143,SRR32025074,SRX27375415,SRS23810879,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 2 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741278,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:wt control|geo loc name:missing|collection date:missing,control 2 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,GSM8741278,GSM8741278: control 2 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741278 r1,GSM8741278,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,12_wt_control_D9_R1.fastq.gz,fastq,1826731050.0,24356414.0,GSM8741278 r1,0:75,A:624589544;C:306590828;G:354308807;T:540924959;N:316912,75,,,,624589544,306590828,354308807,540924959,316912,SRX27375415,SRS23810879,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29144,SRR32025075,SRX27375414,SRS23810878,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 1 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741277,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:wt control|geo loc name:missing|collection date:missing,control 1 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,GSM8741277,GSM8741277: control 1 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741277 r1,GSM8741277,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,11_wt_control_C9_R1.fastq.gz,fastq,1657528425.0,22100379.0,GSM8741277 r1,0:75,A:567762447;C:276623380;G:320467937;T:492394510;N:280151,75,,,,567762447,276623380,320467937,492394510,280151,SRX27375414,SRS23810878,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29677,SRR27406946,SRX23082021,SRS20040790,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 6 s   2 [IL 13 30 32],GSM8001105,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:6 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 6 s   2 [IL 13 30 32],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:6 dpf|tissue:whole embryo/larva,GSM8001105,GSM8001105: m 6 s   2 [IL 13 30 32]; Danio rerio; RNA Seq,GSM8001105 r1,GSM8001105,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-32_CGTACG_L001_R1_001.fastq.gz,fastq,416057592.0,8157992.0,GSM8001105 r1,0:51,A:102142103;C:101373914;G:97024244;T:115471134;N:46197,51,,,,102142103,101373914,97024244,115471134,46197,SRX23082021,SRS20040790,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29678,SRR27406947,SRX23082021,SRS20040790,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 6 s   2 [IL 13 30 32],GSM8001105,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:6 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 6 s   2 [IL 13 30 32],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:6 dpf|tissue:whole embryo/larva,GSM8001105,GSM8001105: m 6 s   2 [IL 13 30 32]; Danio rerio; RNA Seq,GSM8001105 r1,GSM8001105,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-32_CGTACG_L002_R1_001.fastq.gz,fastq,424539249.0,8324299.0,GSM8001105 r2,0:51,A:104318858;C:103391735;G:98951259;T:117859918;N:17479,51,,,,104318858,103391735,98951259,117859918,17479,SRX23082021,SRS20040790,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29679,SRR27406948,SRX23082020,SRS20040788,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 6 s [IL 13 30 31],GSM8001104,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:6 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 6 s [IL 13 30 31],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:6 dpf|tissue:whole embryo/larva,GSM8001104,GSM8001104: p 6 s [IL 13 30 31]; Danio rerio; RNA Seq,GSM8001104 r1,GSM8001104,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-31_GTTTCG_L001_R1_001.fastq.gz,fastq,336956082.0,6606982.0,GSM8001104 r1,0:51,A:81805829;C:82575847;G:78870721;T:93667461;N:36224,51,,,,81805829,82575847,78870721,93667461,36224,SRX23082020,SRS20040788,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29680,SRR27406949,SRX23082020,SRS20040788,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 6 s [IL 13 30 31],GSM8001104,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:6 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 6 s [IL 13 30 31],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:6 dpf|tissue:whole embryo/larva,GSM8001104,GSM8001104: p 6 s [IL 13 30 31]; Danio rerio; RNA Seq,GSM8001104 r1,GSM8001104,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-31_GTTTCG_L002_R1_001.fastq.gz,fastq,343735920.0,6739920.0,GSM8001104 r2,0:51,A:83495446;C:84252532;G:80385387;T:95588863;N:13692,51,,,,83495446,84252532,80385387,95588863,13692,SRX23082020,SRS20040788,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29681,SRR27406950,SRX23082019,SRS20040789,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 4 s [IL 13 30 30],GSM8001103,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 4 s [IL 13 30 30],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva,GSM8001103,GSM8001103: m 4 s [IL 13 30 30]; Danio rerio; RNA Seq,GSM8001103 r1,GSM8001103,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-30_GTGGCC_L001_R1_001.fastq.gz,fastq,325837674.0,6388974.0,GSM8001103 r1,0:51,A:80805848;C:78380749;G:75147290;T:91467315;N:36472,51,,,,80805848,78380749,75147290,91467315,36472,SRX23082019,SRS20040789,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29682,SRR27406951,SRX23082019,SRS20040789,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 4 s [IL 13 30 30],GSM8001103,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 4 s [IL 13 30 30],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva,GSM8001103,GSM8001103: m 4 s [IL 13 30 30]; Danio rerio; RNA Seq,GSM8001103 r1,GSM8001103,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-30_GTGGCC_L002_R1_001.fastq.gz,fastq,333111549.0,6531599.0,GSM8001103 r2,0:51,A:82692565;C:80092634;G:76757552;T:93555769;N:13029,51,,,,82692565,80092634,76757552,93555769,13029,SRX23082019,SRS20040789,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29683,SRR27406952,SRX23082018,SRS20040786,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 4 2 [IL 13 30 29],GSM8001102,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 4 2 [IL 13 30 29],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva,GSM8001102,GSM8001102: m 4 2 [IL 13 30 29]; Danio rerio; RNA Seq,GSM8001102 r1,GSM8001102,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-29_GGCTAC_L001_R1_001.fastq.gz,fastq,197899227.0,3880377.0,GSM8001102 r1,0:51,A:48874076;C:47852911;G:45809628;T:55339675;N:22937,51,,,,48874076,47852911,45809628,55339675,22937,SRX23082018,SRS20040786,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29684,SRR27406953,SRX23082018,SRS20040786,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 4 2 [IL 13 30 29],GSM8001102,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 4 2 [IL 13 30 29],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva,GSM8001102,GSM8001102: m 4 2 [IL 13 30 29]; Danio rerio; RNA Seq,GSM8001102 r1,GSM8001102,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-29_GGCTAC_L002_R1_001.fastq.gz,fastq,201408027.0,3949177.0,GSM8001102 r2,0:51,A:49762966;C:48690671;G:46576512;T:56369616;N:8262,51,,,,49762966,48690671,46576512,56369616,8262,SRX23082018,SRS20040786,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29685,SRR27406954,SRX23082017,SRS20040787,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 4 1 [IL 13 30 28],GSM8001101,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 4 1 [IL 13 30 28],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva,GSM8001101,GSM8001101: m 4 1 [IL 13 30 28]; Danio rerio; RNA Seq,GSM8001101 r1,GSM8001101,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-28_TAGCTT_L001_R1_001.fastq.gz,fastq,238045560.0,4667560.0,GSM8001101 r1,0:51,A:58767746;C:57659215;G:55554391;T:66038681;N:25527,51,,,,58767746,57659215,55554391,66038681,25527,SRX23082017,SRS20040787,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29686,SRR27406955,SRX23082017,SRS20040787,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 4 1 [IL 13 30 28],GSM8001101,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 4 1 [IL 13 30 28],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva,GSM8001101,GSM8001101: m 4 1 [IL 13 30 28]; Danio rerio; RNA Seq,GSM8001101 r1,GSM8001101,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-28_TAGCTT_L002_R1_001.fastq.gz,fastq,242904279.0,4762829.0,GSM8001101 r2,0:51,A:60029401;C:58821065;G:56644387;T:67399896;N:9530,51,,,,60029401,58821065,56644387,67399896,9530,SRX23082017,SRS20040787,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29687,SRR27406956,SRX23082016,SRS20040782,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 4 s [IL 13 30 27],GSM8001100,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 4 s [IL 13 30 27],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva,GSM8001100,GSM8001100: p 4 s [IL 13 30 27]; Danio rerio; RNA Seq,GSM8001100 r1,GSM8001100,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-27_GATCAG_L001_R1_001.fastq.gz,fastq,312793965.0,6133215.0,GSM8001100 r1,0:51,A:77247575;C:75189591;G:71777185;T:88544707;N:34907,51,,,,77247575,75189591,71777185,88544707,34907,SRX23082016,SRS20040782,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29688,SRR27406957,SRX23082016,SRS20040782,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 4 s [IL 13 30 27],GSM8001100,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 4 s [IL 13 30 27],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva,GSM8001100,GSM8001100: p 4 s [IL 13 30 27]; Danio rerio; RNA Seq,GSM8001100 r1,GSM8001100,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-27_GATCAG_L002_R1_001.fastq.gz,fastq,317798238.0,6231338.0,GSM8001100 r2,0:51,A:78561371;C:76374371;G:72870754;T:89978216;N:13526,51,,,,78561371,76374371,72870754,89978216,13526,SRX23082016,SRS20040782,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29689,SRR27406958,SRX23082015,SRS20040784,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 4 2 [IL 13 30 26],GSM8001099,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 4 2  [IL 13 30 26],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva,GSM8001099,GSM8001099: p 4 2  [IL 13 30 26]; Danio rerio; RNA Seq,GSM8001099 r1,GSM8001099,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-26_GAGTGG_L001_R1_001.fastq.gz,fastq,358444983.0,7028333.0,GSM8001099 r1,0:51,A:87990429;C:86848774;G:83282005;T:100282103;N:41672,51,,,,87990429,86848774,83282005,100282103,41672,SRX23082015,SRS20040784,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29690,SRR27406959,SRX23082015,SRS20040784,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 4 2 [IL 13 30 26],GSM8001099,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 4 2  [IL 13 30 26],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva,GSM8001099,GSM8001099: p 4 2  [IL 13 30 26]; Danio rerio; RNA Seq,GSM8001099 r1,GSM8001099,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-26_GAGTGG_L002_R1_001.fastq.gz,fastq,363763671.0,7132621.0,GSM8001099 r2,0:51,A:89389622;C:88080819;G:84463019;T:101815021;N:15190,51,,,,89389622,88080819,84463019,101815021,15190,SRX23082015,SRS20040784,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29691,SRR27406960,SRX23082014,SRS20040783,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 4 1 [IL 13 30 25],GSM8001098,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 4 1 [IL 13 30 25],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva,GSM8001098,GSM8001098: p 4 1 [IL 13 30 25]; Danio rerio; RNA Seq,GSM8001098 r1,GSM8001098,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-25_TTAGGC_L001_R1_001.fastq.gz,fastq,264369975.0,5183725.0,GSM8001098 r1,0:51,A:64903076;C:63955314;G:61111702;T:74374447;N:25436,51,,,,64903076,63955314,61111702,74374447,25436,SRX23082014,SRS20040783,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29692,SRR27406961,SRX23082014,SRS20040783,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 4 1 [IL 13 30 25],GSM8001098,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 4 1 [IL 13 30 25],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva,GSM8001098,GSM8001098: p 4 1 [IL 13 30 25]; Danio rerio; RNA Seq,GSM8001098 r1,GSM8001098,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-25_TTAGGC_L002_R1_001.fastq.gz,fastq,268038864.0,5255664.0,GSM8001098 r2,0:51,A:65881878;C:64831975;G:61904001;T:75410447;N:10563,51,,,,65881878,64831975,61904001,75410447,10563,SRX23082014,SRS20040783,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29693,SRR27406962,SRX23082013,SRS20040785,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 5 s [IL 13 30 24],GSM8001097,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:5 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 5 s [IL 13 30 24],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:5 dpf|tissue:whole embryo/larva,GSM8001097,GSM8001097: m 5 s [IL 13 30 24]; Danio rerio; RNA Seq,GSM8001097 r1,GSM8001097,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-24_GCCAAT_L002_R1_001.fastq.gz,fastq,2222118603.0,43570953.0,GSM8001097 r1,0:51,A:576966145;C:539447551;G:521862134;T:583488671;N:354102,51,,,,576966145,539447551,521862134,583488671,354102,SRX23082013,SRS20040785,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29694,SRR27406963,SRX23082012,SRS20040779,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 3 s [IL 13 30 23],GSM8001096,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:3 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 3 s [IL 13 30 23],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:3 dpf|tissue:whole embryo/larva,GSM8001096,GSM8001096: m 3 s [IL 13 30 23]; Danio rerio; RNA Seq,GSM8001096 r1,GSM8001096,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-23_ACAGTG_L002_R1_001.fastq.gz,fastq,1260954855.0,24724605.0,GSM8001096 r1,0:51,A:326961751;C:306257393;G:300159941;T:327374634;N:201136,51,,,,326961751,306257393,300159941,327374634,201136,SRX23082012,SRS20040779,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29695,SRR27406964,SRX23082011,SRS20040777,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 5 s [IL 13 30 22],GSM8001095,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:5 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 5 s [IL 13 30 22],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:5 dpf|tissue:whole embryo/larva,GSM8001095,GSM8001095: p 5 s [IL 13 30 22]; Danio rerio; RNA Seq,GSM8001095 r1,GSM8001095,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-22_TGACCA_L002_R1_001.fastq.gz,fastq,982727262.0,19269162.0,GSM8001095 r1,0:51,A:254210518;C:239327489;G:233438732;T:255593021;N:157502,51,,,,254210518,239327489,233438732,255593021,157502,SRX23082011,SRS20040777,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29696,SRR27406965,SRX23082010,SRS20040778,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 3 s [IL 13 30 21],GSM8001094,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:3 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 3 s [IL 13 30 21],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:3 dpf|tissue:whole embryo/larva,GSM8001094,GSM8001094: p 3 s [IL 13 30 21]; Danio rerio; RNA Seq,GSM8001094 r1,GSM8001094,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-21_CGATGT_L002_R1_001.fastq.gz,fastq,1037356779.0,20340329.0,GSM8001094 r1,0:51,A:269746979;C:251588766;G:245295859;T:270558757;N:166418,51,,,,269746979,251588766,245295859,270558757,166418,SRX23082010,SRS20040778,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29697,SRR27406966,SRX23082009,SRS20040775,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 8 s [IL 13 30 20],GSM8001093,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:8 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 8 s [IL 13 30 20],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:8 dpf|tissue:whole embryo/larva,GSM8001093,GSM8001093: m 8 s [IL 13 30 20]; Danio rerio; RNA Seq,GSM8001093 r1,GSM8001093,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-20_GGCTAC_L002_R1_001.fastq.gz,fastq,553647228.0,10855828.0,GSM8001093 r1,0:51,A:134883646;C:143513277;G:139480793;T:135331042;N:438470,51,,,,134883646,143513277,139480793,135331042,438470,SRX23082009,SRS20040775,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29698,SRR27406967,SRX23082008,SRS20040776,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,M 8 1 [IL 13 30 19],GSM8001092,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:8 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,M 8 1 [IL 13 30 19],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:8 dpf|tissue:whole embryo/larva,GSM8001092,GSM8001092: M 8 1 [IL 13 30 19]; Danio rerio; RNA Seq,GSM8001092 r1,GSM8001092,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-19_TAGCTT_L002_R1_001.fastq.gz,fastq,62964855.0,1234605.0,GSM8001092 r1,0:51,A:15317447;C:16365148;G:15892573;T:15339413;N:50274,51,,,,15317447,16365148,15892573,15339413,50274,SRX23082008,SRS20040776,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29699,SRR27406968,SRX23082008,SRS20040776,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,M 8 1 [IL 13 30 19],GSM8001092,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:8 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,M 8 1 [IL 13 30 19],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:8 dpf|tissue:whole embryo/larva,GSM8001092,GSM8001092: M 8 1 [IL 13 30 19]; Danio rerio; RNA Seq,GSM8001092 r1,GSM8001092,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-19_TAGCTT_L002_R1_002.fastq.gz,fastq,819926286.0,16076986.0,GSM8001092 r2,0:51,A:200506200;C:212085852;G:207134817;T:200070297;N:129120,51,,,,200506200,212085852,207134817,200070297,129120,SRX23082008,SRS20040776,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29700,SRR27406969,SRX23082007,SRS20040780,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 8 s [IL 13 30 18],GSM8001091,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:8 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 8 s [IL 13 30 18],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:8 dpf|tissue:whole embryo/larva,GSM8001091,GSM8001091: p 8 s [IL 13 30 18]; Danio rerio; RNA Seq,GSM8001091 r1,GSM8001091,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-18_GATCAG_L002_R1_001.fastq.gz,fastq,639923316.0,12547516.0,GSM8001091 r1,0:51,A:163788580;C:157878572;G:152810290;T:164930630;N:515244,51,,,,163788580,157878572,152810290,164930630,515244,SRX23082007,SRS20040780,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29701,SRR27406970,SRX23082006,SRS20040781,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 8 1 [IL 13 30 17],GSM8001090,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:8 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 8 1 [IL 13 30 17],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:8 dpf|tissue:whole embryo/larva,GSM8001090,GSM8001090: p 8 1 [IL 13 30 17]; Danio rerio; RNA Seq,GSM8001090 r1,GSM8001090,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-17_ACTTGA_L002_R1_001.fastq.gz,fastq,586754847.0,11504997.0,GSM8001090 r1,0:51,A:144643558;C:150218708;G:146661023;T:144769661;N:461897,51,,,,144643558,150218708,146661023,144769661,461897,SRX23082006,SRS20040781,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29702,SRR27406971,SRX23082005,SRS20040774,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 6 s [IL 13 30 16],GSM8001089,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:6 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 6 s [IL 13 30 16],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:6 dpf|tissue:whole embryo/larva,GSM8001089,GSM8001089: m 6 s [IL 13 30 16]; Danio rerio; RNA Seq,GSM8001089 r1,GSM8001089,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-16_TTAGGC_L002_R1_001.fastq.gz,fastq,443064948.0,8687548.0,GSM8001089 r1,0:51,A:111215571;C:111682539;G:108653697;T:111157539;N:355602,51,,,,111215571,111682539,108653697,111157539,355602,SRX23082005,SRS20040774,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29703,SRR27406972,SRX23082004,SRS20040773,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 6 1 [IL 13 30 15],GSM8001088,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:6 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 6 1 [IL 13 30 15],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:6 dpf|tissue:whole embryo/larva,GSM8001088,GSM8001088: m 6 1 [IL 13 30 15]; Danio rerio; RNA Seq,GSM8001088 r1,GSM8001088,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-15_ATCACG_L002_R1_001.fastq.gz,fastq,882129252.0,17296652.0,GSM8001088 r1,0:51,A:232882429;C:211887994;G:201698856;T:234945732;N:714241,51,,,,232882429,211887994,201698856,234945732,714241,SRX23082004,SRS20040773,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29704,SRR27406973,SRX23082003,SRS20040770,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 6 2 [IL 13 30 14],GSM8001087,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:6 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 6 2 [IL 13 30 14],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:6 dpf|tissue:whole embryo/larva,GSM8001087,GSM8001087: p 6 2 [IL 13 30 14]; Danio rerio; RNA Seq,GSM8001087 r1,GSM8001087,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-14_GTGAAA_L002_R1_001.fastq.gz,fastq,547226022.0,10729922.0,GSM8001087 r1,0:51,A:132788152;C:142246667;G:138933647;T:132816349;N:441207,51,,,,132788152,142246667,138933647,132816349,441207,SRX23082003,SRS20040770,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29705,SRR27406974,SRX23082002,SRS20040769,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 6 1 [IL 13 30 13],GSM8001086,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:6 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 6 1 [IL 13 30 13],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:6 dpf|tissue:whole embryo/larva,GSM8001086,GSM8001086: p 6 1 [IL 13 30 13]; Danio rerio; RNA Seq,GSM8001086 r1,GSM8001086,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-13_GTCCGC_L002_R1_001.fastq.gz,fastq,520266810.0,10201310.0,GSM8001086 r1,0:51,A:125933056;C:135555201;G:132217921;T:126145133;N:415499,51,,,,125933056,135555201,132217921,126145133,415499,SRX23082002,SRS20040769,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29706,SRR27406975,SRX23082001,SRS20040772,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 5 2 [IL 13 30 12],GSM8001085,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:5 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 5 2 [IL 13 30 12],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:5 dpf|tissue:whole embryo/larva,GSM8001085,GSM8001085: m 5 2 [IL 13 30 12]; Danio rerio; RNA Seq,GSM8001085 r1,GSM8001085,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-12_CCGTCC_L002_R1_001.fastq.gz,fastq,580544118.0,11383218.0,GSM8001085 r1,0:51,A:147287127;C:144405857;G:140535839;T:147847352;N:467943,51,,,,147287127,144405857,140535839,147847352,467943,SRX23082001,SRS20040772,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29707,SRR27406976,SRX23082000,SRS20040771,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 5 1 [IL 13 30 11],GSM8001084,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:5 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 5 1 [IL 13 30 11],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:5 dpf|tissue:whole embryo/larva,GSM8001084,GSM8001084: m 5 1 [IL 13 30 11]; Danio rerio; RNA Seq,GSM8001084 r1,GSM8001084,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-11_ATGTCA_L002_R1_001.fastq.gz,fastq,575366394.0,11281694.0,GSM8001084 r1,0:51,A:149073331;C:140502112;G:136425599;T:148905317;N:460035,51,,,,149073331,140502112,136425599,148905317,460035,SRX23082000,SRS20040771,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29708,SRR27406977,SRX23081999,SRS20040767,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 5 2 [IL 13 30 10],GSM8001083,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:5 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 5 2 [IL 13 30 10],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:5 dpf|tissue:whole embryo/larva,GSM8001083,GSM8001083: p 5 2 [IL 13 30 10]; Danio rerio; RNA Seq,GSM8001083 r1,GSM8001083,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-10_AGTTCC_L001_R1_001.fastq.gz,fastq,542919888.0,10645488.0,GSM8001083 r1,0:51,A:138706445;C:133885327;G:130561786;T:139292916;N:473414,51,,,,138706445,133885327,130561786,139292916,473414,SRX23081999,SRS20040767,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29709,SRR27406978,SRX23081998,SRS20040768,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 5 1 [IL 13 30 9],GSM8001082,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:5 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 5 1 [IL 13 30 9],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:5 dpf|tissue:whole embryo/larva,GSM8001082,GSM8001082: p 5 1 [IL 13 30 9]; Danio rerio; RNA Seq,GSM8001082 r1,GSM8001082,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-9_AGTCAA_L001_R1_001.fastq.gz,fastq,452635557.0,8875207.0,GSM8001082 r1,0:51,A:116752949;C:110829948;G:107471046;T:117187118;N:394496,51,,,,116752949,110829948,107471046,117187118,394496,SRX23081998,SRS20040768,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29710,SRR27406979,SRX23081997,SRS20040765,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 3 2 [IL 13 30 8],GSM8001081,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:3 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 3 2 [IL 13 30 8],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:3 dpf|tissue:whole embryo/larva,GSM8001081,GSM8001081: m 3 2 [IL 13 30 8]; Danio rerio; RNA Seq,GSM8001081 r1,GSM8001081,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-8_CTTGTA_L001_R1_001.fastq.gz,fastq,489962100.0,9607100.0,GSM8001081 r1,0:51,A:126576626;C:120177833;G:115721569;T:127054827;N:431245,51,,,,126576626,120177833,115721569,127054827,431245,SRX23081997,SRS20040765,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29711,SRR27406980,SRX23081996,SRS20040763,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m3 1 [IL 13 30 7],GSM8001080,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:3 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m3 1 [IL 13 30 7],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:3 dpf|tissue:whole embryo/larva,GSM8001080,GSM8001080: m3 1 [IL 13 30 7]; Danio rerio; RNA Seq,GSM8001080 r1,GSM8001080,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-7_CAGATC_L001_R1_001.fastq.gz,fastq,508392072.0,9968472.0,GSM8001080 r1,0:51,A:131266675;C:124519771;G:120906726;T:131244280;N:454620,51,,,,131266675,124519771,120906726,131244280,454620,SRX23081996,SRS20040763,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29712,SRR27406981,SRX23081995,SRS20040762,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 3 2 [IL 13 30 6],GSM8001079,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:3 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 3 2 [IL 13 30 6],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:3 dpf|tissue:whole embryo/larva,GSM8001079,GSM8001079: p 3 2 [IL 13 30 6]; Danio rerio; RNA Seq,GSM8001079 r1,GSM8001079,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-6_GCCAAT_L001_R1_001.fastq.gz,fastq,453386736.0,8889936.0,GSM8001079 r1,0:51,A:116163394;C:112054233;G:108633583;T:116138053;N:397473,51,,,,116163394,112054233,108633583,116138053,397473,SRX23081995,SRS20040762,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29713,SRR27406982,SRX23081994,SRS20040761,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 3 1 [IL 13 30 5],GSM8001078,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:3 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 3 1 [IL 13 30 5],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:3 dpf|tissue:whole embryo/larva,GSM8001078,GSM8001078: p 3 1 [IL 13 30 5]; Danio rerio; RNA Seq,GSM8001078 r1,GSM8001078,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-5_ACAGTG_L001_R1_001.fastq.gz,fastq,527854335.0,10350085.0,GSM8001078 r1,0:51,A:136133452;C:129943239;G:125251939;T:136062979;N:462726,51,,,,136133452,129943239,125251939,136062979,462726,SRX23081994,SRS20040761,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29714,SRR27406983,SRX23081993,SRS20040766,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 0 s [IL 13 30 4],GSM8001077,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:0 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 0 s [IL 13 30 4],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:0 dpf|tissue:whole embryo/larva,GSM8001077,GSM8001077: m 0 s [IL 13 30 4]; Danio rerio; RNA Seq,GSM8001077 r1,GSM8001077,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-4_TGACCA_L001_R1_001.fastq.gz,fastq,498889140.0,9782140.0,GSM8001077 r1,0:51,A:129822030;C:121205451;G:117439534;T:129980097;N:442028,51,,,,129822030,121205451,117439534,129980097,442028,SRX23081993,SRS20040766,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures