{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Multi-stage\"", "rows": [[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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, 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", null, "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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, 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", null, "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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, 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", null, "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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, 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", null, "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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, 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", null, "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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, 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", null, "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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, 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", null, "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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, 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", null, "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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, 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", null, "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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, 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", null, "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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, 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", null, "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", null, null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 353294009, 340727934, 322476371, 393200193, 441043, "ERX2160152", "ERS1883528", "ERA1011308", "Fundacao Champalimaud|European Nucleotide Archive", "Fundacao Champalimaud|European Nucleotide Archive", 1, 0.95434, null, 0.08906, null, 0.66935, null, 0.47788, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 369453299, 359092235, 341176884, 408389810, 508940, "ERX2160151", "ERS1883527", "ERA1011308", "Fundacao Champalimaud|European Nucleotide Archive", "Fundacao Champalimaud|European Nucleotide Archive", 1, 0.95582, null, 0.08202, null, 0.67718, null, 0.47812, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 386600603, 373317031, 350339456, 420938891, 517200, "ERX2160150", "ERS1883526", "ERA1011308", "Fundacao Champalimaud|European Nucleotide Archive", "Fundacao Champalimaud|European Nucleotide Archive", 1, 0.9552, null, 0.08124, null, 0.67685, null, 0.47578, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 345997031, 338444594, 316575258, 379195977, 449148, "ERX2160149", "ERS1883525", "ERA1011308", "Fundacao Champalimaud|European Nucleotide Archive", "Fundacao Champalimaud|European Nucleotide Archive", 1, 0.95615, null, 0.08131, null, 0.68694, null, 0.45267, null, 74, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 338213530, 326808990, 303983789, 367147896, 486530, "ERX2160148", "ERS1883524", "ERA1011308", "Fundacao Champalimaud|European Nucleotide Archive", "Fundacao Champalimaud|European Nucleotide Archive", 1, 0.95427, null, 0.08628, null, 0.67706, null, 0.47245, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 322048172, 316542683, 299227724, 359449433, 426833, "ERX2160147", "ERS1883523", "ERA1011308", "Fundacao Champalimaud|European Nucleotide Archive", "Fundacao Champalimaud|European Nucleotide Archive", 1, 0.95505, null, 0.08541, null, 0.67659, null, 0.48159, null, 75, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Portugal", "2017-08-23", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [9892, "ERR4172795", "ERX4136409", "ERS4580819", "ERP121885", "PRJEB38455", "RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "E-MTAB-9113", "Transcriptome Analysis", "RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants", "ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22", null, "Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion", "sibling 3", "SAMEA6853229", "Centre for Developmental Neurobiology King's College London", "ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853229|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sibling 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|sample name:E MTAB 9113:sibling 3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "E MTAB 9113:sibling 3 p", "sibling 3 p", "RNA 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 constructed with ribodepletion", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP121885", "Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19", "UCLGNS1141-gfp-sibs-3_S6_R1.fastq.gz UCLGNS1141-gfp-sibs-3_S6_R2.fastq.gz", "fastq fastq", null, null, "E MTAB 9113:UCLGNS1141 gfp sibs 3 S6 R", "0:81 1:81", "A:1144578958;C:1113109875;G:1138809559;T:1117038434;N:213932", 81, 81, null, null, 1144578958, 1113109875, 1138809559, 1117038434, 213932, "ERX4136409", "ERS4580819", "ERA2625401", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 2, 0.96684, 0.96492, 0.03244, 0.0317, 0.71236, 0.71514, 0.45871, 0.46189, 81, 81, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-05-22", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [9893, "ERR4172794", "ERX4136408", "ERS4580818", "ERP121885", "PRJEB38455", "RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "E-MTAB-9113", "Transcriptome Analysis", "RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants", "ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22", null, "Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion", "sibling 2", "SAMEA6853228", "Centre for Developmental Neurobiology King's College London", "ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853228|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sibling 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|sample name:E MTAB 9113:sibling 2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "E MTAB 9113:sibling 2 p", "sibling 2 p", "RNA 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 constructed with ribodepletion", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP121885", "Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19", "UCLGNS1141-gfp-sibs-2_S4_R1.fastq.gz UCLGNS1141-gfp-sibs-2_S4_R2.fastq.gz", "fastq fastq", null, null, "E MTAB 9113:UCLGNS1141 gfp sibs 2 S4 R", "0:81 1:81", "A:1056280368;C:1036355469;G:1045429486;T:1035773622;N:189389", 81, 81, null, null, 1056280368, 1036355469, 1045429486, 1035773622, 189389, "ERX4136408", "ERS4580818", "ERA2625401", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 2, 0.95511, 0.95696, 0.02941, 0.02903, 0.71492, 0.71628, 0.45765, 0.46537, 81, 81, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-05-22", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [9894, "ERR4172793", "ERX4136407", "ERS4580817", "ERP121885", "PRJEB38455", "RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "E-MTAB-9113", "Transcriptome Analysis", "RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants", "ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22", null, "Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion", "sibling 1", "SAMEA6853227", "Centre for Developmental Neurobiology King's College London", "ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853227|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sibling 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|sample name:E MTAB 9113:sibling 1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "E MTAB 9113:sibling 1 p", "sibling 1 p", "RNA 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 constructed with ribodepletion", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP121885", "Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19", "UCLGNS1141-gfp-sibs-1_S2_R1.fastq.gz UCLGNS1141-gfp-sibs-1_S2_R2.fastq.gz", "fastq fastq", null, null, "E MTAB 9113:UCLGNS1141 gfp sibs 1 S2 R", "0:81 1:81", "A:1121176859;C:1093927654;G:1108608188;T:1101082277;N:209264", 81, 81, null, null, 1121176859, 1093927654, 1108608188, 1101082277, 209264, "ERX4136407", "ERS4580817", "ERA2625401", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 2, 0.95795, 0.96004, 0.02885, 0.02854, 0.71648, 0.71756, 0.44348, 0.43956, 81, 81, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-05-22", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [9895, "ERR4172792", "ERX4136406", "ERS4580816", "ERP121885", "PRJEB38455", "RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "E-MTAB-9113", "Transcriptome Analysis", "RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants", "ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22", null, "Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion", "sfpq 3", "SAMEA6853226", "Centre for Developmental Neurobiology King's College London", "ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853226|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sfpq 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:sfpq / |sample name:E MTAB 9113:sfpq 3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "E MTAB 9113:sfpq 3 p", "sfpq 3 p", "RNA 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 constructed with ribodepletion", "Experimental Factor: genotype:sfpq / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP121885", "Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19", "UCLGNS1141-gfp-neg_3_S5_R1.fastq.gz UCLGNS1141-gfp-neg_3_S5_R2.fastq.gz", "fastq fastq", null, null, "E MTAB 9113:UCLGNS1141 gfp neg 3 S5 R", "0:81 1:81", "A:845849249;C:772302798;G:911660213;T:787409272;N:154042", 81, 81, null, null, 845849249, 772302798, 911660213, 787409272, 154042, "ERX4136406", "ERS4580816", "ERA2625401", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 2, 0.96298, 0.95486, 0.03415, 0.03476, 0.7167, 0.73503, 0.4665, 0.45947, 81, 81, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-05-22", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [9896, "ERR4172791", "ERX4136405", "ERS4580815", "ERP121885", "PRJEB38455", "RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "E-MTAB-9113", "Transcriptome Analysis", "RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants", "ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22", null, "Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion", "sfpq 2", "SAMEA6853225", "Centre for Developmental Neurobiology King's College London", "ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853225|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sfpq 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:sfpq / |sample name:E MTAB 9113:sfpq 2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "E MTAB 9113:sfpq 2 p", "sfpq 2 p", "RNA 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 constructed with ribodepletion", "Experimental Factor: genotype:sfpq / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP121885", "Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19", "UCLGNS1141-gfp-neg-2_S3_R1.fastq.gz UCLGNS1141-gfp-neg-2_S3_R2.fastq.gz", "fastq fastq", null, null, "E MTAB 9113:UCLGNS1141 gfp neg 2 S3 R", "0:81 1:81", "A:961156886;C:917011292;G:942713581;T:936109877;N:157724", 81, 81, null, null, 961156886, 917011292, 942713581, 936109877, 157724, "ERX4136405", "ERS4580815", "ERA2625401", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 2, 0.96276, 0.96147, 0.03436, 0.03382, 0.71892, 0.72021, 0.4581, 0.46402, 81, 81, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-05-22", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [9897, "ERR4172790", "ERX4136404", "ERS4580814", "ERP121885", "PRJEB38455", "RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "E-MTAB-9113", "Transcriptome Analysis", "RNA was extracted from whole zebrafish embryos at 24 hpf to examine changes in gene expression and splicing in sfpq null mutants", "ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 05 22", null, "Protocols: Embryos were collected from in crosses of sfpq+/ adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library constructed with ribodepletion", "sfpq 1", "SAMEA6853224", "Centre for Developmental Neurobiology King's College London", "ENA FIRST PUBLIC:2020 12 01T04:08:08Z|ENA LAST UPDATE:2020 05 22T17:13:15Z|External Id:SAMEA6853224|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2020 12 01T04:08:08Z|INSDC last update:2020 05 22T17:13:15Z|INSDC status:public|Submitter Id:E MTAB 9113:sfpq 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:sfpq / |sample name:E MTAB 9113:sfpq 1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "E MTAB 9113:sfpq 1 p", "sfpq 1 p", "RNA 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 constructed with ribodepletion", "Experimental Factor: genotype:sfpq / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP121885", "Illumina HiSeq 2500 paired end sequencing; RNA seq of sfpq / zebrafish embryos and siblings at 24 hpf", "ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 06 19", "UCLGNS1141-gfp-neg-1_S1_R1.fastq.gz UCLGNS1141-gfp-neg-1_S1_R2.fastq.gz", "fastq fastq", null, null, "E MTAB 9113:UCLGNS1141 gfp neg 1 S1 R", "0:81 1:81", "A:1046317524;C:1014946275;G:1036910299;T:1023619857;N:185237", 81, 81, null, null, 1046317524, 1014946275, 1036910299, 1023619857, 185237, "ERX4136404", "ERS4580814", "ERA2625401", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 2, 0.96015, 0.96173, 0.03114, 0.03098, 0.7175, 0.71865, 0.46666, 0.46399, 81, 81, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-05-22", "Multi-stage", "Multi-stage", "Embryo Imprecise", "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "E MTAB 9899:sibling 3", "0:76 1:0", "A:385382600;C:210104151;G:238678838;T:315495923;N:5536", 76, 0, null, null, 385382600, 210104151, 238678838, 315495923, 5536, "ERX4792138", "ERS5459722", "ERA3194022", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 1, 0.82613, null, 0.13111, null, 0.77597, null, 0.53833, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "other", "lexogen", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "E MTAB 9899:sibling 2", "0:76 1:0", "A:405337161;C:226099266;G:255734601;T:341120121;N:5955", 76, 0, null, null, 405337161, 226099266, 255734601, 341120121, 5955, "ERX4792137", "ERS5459721", "ERA3194022", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 1, 0.84066, null, 0.12241, null, 0.77755, null, 0.56472, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "other", "lexogen", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "E MTAB 9899:sibling 1", "0:76 1:0", "A:440539801;C:236835299;G:268057277;T:355636994;N:6169", 76, 0, null, null, 440539801, 236835299, 268057277, 355636994, 6169, "ERX4792136", "ERS5459720", "ERA3194022", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 1, 0.82002, null, 0.12908, null, 0.77766, null, 0.54981, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "other", "lexogen", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "E MTAB 9899:sfpq 3", "0:76 1:0", "A:493165327;C:268347233;G:303443918;T:399152596;N:7138", 76, 0, null, null, 493165327, 268347233, 303443918, 399152596, 7138, "ERX4792135", "ERS5459719", "ERA3194022", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 1, 0.82521, null, 0.12349, null, 0.78545, null, 0.57446, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "other", "lexogen", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "E MTAB 9899:sfpq 2", "0:76 1:0", "A:426637005;C:227027693;G:257342561;T:338159540;N:5909", 76, 0, null, null, 426637005, 227027693, 257342561, 338159540, 5909, "ERX4792134", "ERS5459718", "ERA3194022", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 1, 0.81933, null, 0.11571, null, 0.78593, null, 0.56675, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "other", "lexogen", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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", null, null, "E MTAB 9899:sfpq 1", "0:76 1:0", "A:425613638;C:225707961;G:254738302;T:336863560;N:5847", 76, 0, null, null, 425613638, 225707961, 254738302, 336863560, 5847, "ERX4792133", "ERS5459717", "ERA3194022", "Centre for Developmental Neurobiology King", "Centre for Developmental Neurobiology King", 1, 0.81857, null, 0.11342, null, 0.78587, null, 0.56439, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "other", "lexogen", "bulk", "unknown", "unknown", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "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", null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. 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 \u00b1 2 \u00b0C and a 12:12 light/dark cycle at the Fraunhofer Institute for molecular biology and applied ecology IME Schmallenberg Germany. TetraMin\u00ae 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 \u00b1 1 \u00b0C until further use. Fish embryo incubation: Embryos were incubated at a controlled temperature of 26 \u00b1 1\u00b0C 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 \u201ctreatment protocol\u201d Clobetasol propionate 21 Chlor 9 fluor 11\u03b2 17 dihydroxy 16\u03b2 methylpregna 1 4 dien 3 20 dion 17 propionat purity \u2265 98 % CAS no. 25122 46 7 and Imiquimod 1 2 methylpropyl 1H imidazo[4 5 c]quinoline 4 amine purity \u2265 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 \u00b5l 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 \u00b5l 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 \u00b5l 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 \u2265 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 \u00b1 1\u00b0C 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 D\u00fcren Germany. Briefly frozen embryos were transferred to screw cap tubes filled with 350 \u00b5l 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\u00b0C 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 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", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [25298, "SRR25764100", "SRX21486771", "SRS18719071", "SRP457109", "PRJNA1009810", "Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish", "GSE241757", "Transcriptome Analysis", "Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.", null, "pubmed:38265193", null, "1 dpf itgb4+ embryonic basal precursors rep2", "GSM7734878", null, "tissue:epidermal cells|cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing", "1 dpf itgb4+ embryonic basal precursors rep2", "High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values.", "epidermal cells", "Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer\u2019s protocol.", "Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 \u00b0C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.", "cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry", "GSM7734878", "GSM7734878: 1 dpf itgb4+ embryonic basal precursors rep2; Danio rerio; RNA Seq", "GSM7734878 r1", "GSM7734878", "1", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP457109", null, null, "itgb4mcherry_2_S229_R1_001.fastq.gz itgb4mcherry_2_S229_R2_001.fastq.gz", "fastq fastq", 6040245600.0, 15100614.0, "GSM7734878 r1", "0:200 1:200", "A:1588346322;C:1356558310;G:1524614760;T:1569583583;N:1142625", 200, 200, null, null, 1588346322, 1356558310, 1524614760, 1569583583, 1142625, "SRX21486771", "SRS18719071", "SRA1700438", "Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology", "Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology", 2, 0.0156, 0.0191, 0.00074, 0.00093, 0.99024, 0.99088, 0.47058, 0.47838, 200, 200, "T", "T", "mates < 9% mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-08-28", "Multi-stage", "Multi-stage", "Skin", "Surface Structure"], [25299, "SRR25764101", "SRX21486770", "SRS18719070", "SRP457109", "PRJNA1009810", "Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish", "GSE241757", "Transcriptome Analysis", "Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.", null, "pubmed:38265193", null, "1 dpf itgb4+ embryonic basal precursors rep1", "GSM7734877", null, "tissue:epidermal cells|cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing", "1 dpf itgb4+ embryonic basal precursors rep1", "High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values.", "epidermal cells", "Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer\u2019s protocol.", "Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 \u00b0C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.", "cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry", "GSM7734877", "GSM7734877: 1 dpf itgb4+ embryonic basal precursors rep1; Danio rerio; RNA Seq", "GSM7734877 r1", "GSM7734877", "1", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP457109", null, null, "itgb4mcherry_1_S20_R1_001.fastq.gz itgb4mcherry_1_S20_R2_001.fastq.gz", "fastq fastq", 7055215600.0, 17638039.0, "GSM7734877 r1", "0:200 1:200", "A:1894635584;C:1556854856;G:1769420212;T:1825520802;N:8784146", 200, 200, null, null, 1894635584, 1556854856, 1769420212, 1825520802, 8784146, "SRX21486770", "SRS18719070", "SRA1700438", "Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology", "Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology", 2, 0.01135, 0.01881, 0.00043, 0.00016, 0.9932, 0.99543, 0.46234, 0.43106, 200, 200, "T", "T", "mates < 9% mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-08-28", "Multi-stage", "Multi-stage", "Skin", "Surface Structure"], [25300, "SRR25764102", "SRX21486769", "SRS18719069", "SRP457109", "PRJNA1009810", "Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish", "GSE241757", "Transcriptome Analysis", "Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.", null, "pubmed:38265193", null, "1 dpf krt4+ embryonic periderm cells rep2", "GSM7734876", null, "tissue:epidermal cells|cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp|geo loc name:missing|collection date:missing", "1 dpf krt4+ embryonic periderm cells rep2", "High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values.", "epidermal cells", "Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer\u2019s protocol.", "Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 \u00b0C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.", "cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp", "GSM7734876", "GSM7734876: 1 dpf krt4+ embryonic periderm cells rep2; Danio rerio; RNA Seq", "GSM7734876 r1", "GSM7734876", "1", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP457109", null, null, "krt4cre-gfp_2_S4_R2_001.fastq.gz krt4cre-gfp_2_S4_R1_001.fastq.gz", "fastq fastq", 9439207600.0, 23598019.0, "GSM7734876 r1", "0:200 1:200", "A:2499982675;C:2086665360;G:2395002073;T:2454282285;N:3275207", 200, 200, null, null, 2499982675, 2086665360, 2395002073, 2454282285, 3275207, "SRX21486769", "SRS18719069", "SRA1700438", "Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology", "Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology", 2, 0.44931, 0.01877, 0.02236, 0.00115, 0.80012, 0.99032, 0.45473, 0.49453, 200, 200, "B", "T", "mate2 technical by mapping diff", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-08-28", "Multi-stage", "Multi-stage", "Skin", "Surface Structure"], [25301, "SRR25764103", "SRX21486768", "SRS18719066", "SRP457109", "PRJNA1009810", "Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish", "GSE241757", "Transcriptome Analysis", "Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.", null, "pubmed:38265193", null, "1 dpf krt4+ embryonic periderm cells rep1", "GSM7734875", null, "tissue:epidermal cells|cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp|geo loc name:missing|collection date:missing", "1 dpf krt4+ embryonic periderm cells rep1", "High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values.", "epidermal cells", "Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer\u2019s protocol.", "Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 \u00b0C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.", "cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp", "GSM7734875", "GSM7734875: 1 dpf krt4+ embryonic periderm cells rep1; Danio rerio; RNA Seq", "GSM7734875 r1", "GSM7734875", "1", "The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy\u2122 WES rapid library preparation kit according to the manufacturer's protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP457109", null, null, "krt4cre-gfp_1_S19_R2_001.fastq.gz krt4cre-gfp_1_S19_R1_001.fastq.gz", "fastq fastq", 6119547200.0, 15298868.0, "GSM7734875 r1", "0:200 1:200", "A:1642059769;C:1349462427;G:1535937964;T:1584527048;N:7559992", 200, 200, null, null, 1642059769, 1349462427, 1535937964, 1584527048, 7559992, "SRX21486768", "SRS18719066", "SRA1700438", "Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology", "Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology", 2, 0.01112, 0.01017, 0.0003, 0.00014, 0.9931, 0.99586, 0.43605, 0.40821, 200, 200, "T", "T", "mates < 9% mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2023-08-28", "Multi-stage", "Multi-stage", "Skin", "Surface Structure"], [26016, "SRR25868588", "SRX21589851", "SRS18767424", "SRP457982", "PRJNA1011844", "Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds", "PRJNA1011844", "Other", "The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature bioaccumulation in organisms and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active in addition to the toxicity endpoints that best reflect chemical hazard. In this study zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control 1uM chlorpyrifos CAS 2921 88 2 positive control and eight concentrations 0 100 uM half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1 PFOA CAS 45285 51 6 and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf 6 hpf 48 hpf 24 hpf 48 hpf 6 hpf 120 hpf 24 hpf 120 hpf 48 hpf 120 hpf 96 hpf 120 hpf to assess how common experimental design variables e.g. different exposure durations exposure at different developmental stages affect point of departure estimates.", null, null, null, null, "T5VAa5", null, "strain:AB wild type|age:24 hpf 120 hpf|dev stage:embryo|collection date:2022|geo loc name:USA: Minnesota Duluth|sex:not applicable|tissue:whole body zebrafish embryo|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division 6201 Congdon Blvd Duluth MN 55876|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 \u00b1 1\u00b0C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5\u00b0C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.|collected by:Great Lakes Toxicology & Ecology Division|sample type:Total RNA|time code:5|dose:0|dose units:ug/L|treatment:VehicleControl|replicate ID:rep2|repeat sample:No|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of danio rerio: whole organism embryo control", "T5VAa5 S217", "T5VAa5 S217", "At the end of each PFAS exposure period zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457982", null, null, "T5VAa5_S217_L002_R1_001.fastq.gz T5VAa5_S217_L002_R2_001.fastq.gz", "fastq fastq", 8100529500.0, 27001765.0, "T5VAa5 S217 L002 R1 001.fastq.gz", "0:150 1:150", "A:2094646242;C:1839873833;G:2144213073;T:2021734883;N:61469", 150, 150, null, null, 2094646242, 1839873833, 2144213073, 2021734883, 61469, "SRX21589851", "SRS18767424", "SRA1703738", "U.S. Environmental Protection Agency|Great Lakes Toxicology and Ecology Division", "U.S. Environmental Protection Agency", 2, 0.61505, 0.62102, 0.08204, 0.08402, 0.72581, 0.72545, 0.499, 0.50086, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2023-09-01", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [29041, "SRR26990794", "SRX22683825", "SRS19677539", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "WT gut3", "GSM7924158", null, "source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing", "WT gut3", "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.", "gut", "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\u00ae 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\u00b0C. 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\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:gut|genotype:wildtype|time:50dpf", "GSM7924158", "GSM7924158: WT gut3; Danio rerio; RNA Seq", "GSM7924158 r1", "GSM7924158", "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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "12_WT_3G_S27_L001_R2_001.fastq.gz 12_WT_3G_S27_L001_R1_001.fastq.gz", "fastq fastq", 6066709786.0, 20088443.0, "GSM7924158 r1", "0:151 1:151", "A:1673762656;C:1360901090;G:1385125931;T:1646863953;N:56156", 151, 151, null, null, 1673762656, 1360901090, 1385125931, 1646863953, 56156, "SRX22683825", "SRS19677539", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.92515, 0.9297, 0.0691, 0.0659, 0.75041, 0.75022, 0.53007, 0.53064, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Gut", "Digestive System"], [29042, "SRR26990795", "SRX22683824", "SRS19677538", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "WT gut2", "GSM7924157", null, "source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing", "WT gut2", "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.", "gut", "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\u00ae 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\u00b0C. 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\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:gut|genotype:wildtype|time:50dpf", "GSM7924157", "GSM7924157: WT gut2; Danio rerio; RNA Seq", "GSM7924157 r1", "GSM7924157", "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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "11_WT_2G_S26_L001_R2_001.fastq.gz 11_WT_2G_S26_L001_R1_001.fastq.gz", "fastq fastq", 5406867570.0, 17903535.0, "GSM7924157 r1", "0:151 1:151", "A:1464846243;C:1237183908;G:1259215309;T:1445572498;N:49612", 151, 151, null, null, 1464846243, 1237183908, 1259215309, 1445572498, 49612, "SRX22683824", "SRS19677538", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.93795, 0.94322, 0.05952, 0.05592, 0.75933, 0.75887, 0.54179, 0.53451, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Gut", "Digestive System"], [29043, "SRR26990796", "SRX22683823", "SRS19677537", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "WT gut1", "GSM7924156", null, "source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing", "WT gut1", "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.", "gut", "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\u00ae 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\u00b0C. 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\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:gut|genotype:wildtype|time:50dpf", "GSM7924156", "GSM7924156: WT gut1; Danio rerio; RNA Seq", "GSM7924156 r1", "GSM7924156", "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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "10_WT_1G_S25_L001_R1_001.fastq.gz 10_WT_1G_S25_L001_R2_001.fastq.gz", "fastq fastq", 5162192908.0, 17093354.0, "GSM7924156 r1", "0:151 1:151", "A:1404682153;C:1175657030;G:1196829496;T:1384975886;N:48343", 151, 151, null, null, 1404682153, 1175657030, 1196829496, 1384975886, 48343, "SRX22683823", "SRS19677537", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.93119, 0.93585, 0.06122, 0.05809, 0.74757, 0.74757, 0.54124, 0.54417, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Gut", "Digestive System"], [29044, "SRR26990797", "SRX22683822", "SRS19677536", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "itgavKO gut3", "GSM7924155", null, "source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing", "itgavKO gut3", "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.", "gut", "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\u00ae 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\u00b0C. 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\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:gut|genotype:itgavKO mutant|time:50dpf", "GSM7924155", "GSM7924155: itgavKO gut3; Danio rerio; RNA Seq", "GSM7924155 r1", "GSM7924155", "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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "9_itgavKO_3G_S24_L001_R2_001.fastq.gz 9_itgavKO_3G_S24_L001_R1_001.fastq.gz", "fastq fastq", 4146743578.0, 13730939.0, "GSM7924155 r1", "0:151 1:151", "A:1130002132;C:943522869;G:958031732;T:1115146458;N:40387", 151, 151, null, null, 1130002132, 943522869, 958031732, 1115146458, 40387, "SRX22683822", "SRS19677536", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.93764, 0.94144, 0.05938, 0.05594, 0.7553, 0.75485, 0.55535, 0.55018, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Gut", "Digestive System"], [29045, "SRR26990798", "SRX22683821", "SRS19677535", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "itgavKO gut2", "GSM7924154", null, "source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing", "itgavKO gut2", "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.", "gut", "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\u00ae 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\u00b0C. 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\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:gut|genotype:itgavKO mutant|time:50dpf", "GSM7924154", "GSM7924154: itgavKO gut2; Danio rerio; RNA Seq", "GSM7924154 r1", "GSM7924154", "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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "8_itgavKO_2G_S23_L001_R1_001.fastq.gz 8_itgavKO_2G_S23_L001_R2_001.fastq.gz", "fastq fastq", 4225756140.0, 13992570.0, "GSM7924154 r1", "0:151 1:151", "A:1133211420;C:974497998;G:995876972;T:1122129220;N:40530", 151, 151, null, null, 1133211420, 974497998, 995876972, 1122129220, 40530, "SRX22683821", "SRS19677535", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.95341, 0.95884, 0.05109, 0.04883, 0.77542, 0.77368, 0.51301, 0.50704, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Gut", "Digestive System"], [29046, "SRR26990799", "SRX22683820", "SRS19677534", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "itagvKO gut1", "GSM7924153", null, "source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing", "itagvKO gut1", "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.", "gut", "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\u00ae 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\u00b0C. 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\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:gut|genotype:itgavKO mutant|time:50dpf", "GSM7924153", "GSM7924153: itagvKO gut1; Danio rerio; RNA Seq", "GSM7924153 r1", "GSM7924153", "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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "7_itagvKO_1G_S22_L001_R1_001.fastq.gz 7_itagvKO_1G_S22_L001_R2_001.fastq.gz", "fastq fastq", 5954117844.0, 19715622.0, "GSM7924153 r1", "0:151 1:151", "A:1600496071;C:1372939932;G:1393534700;T:1587094282;N:52859", 151, 151, null, null, 1600496071, 1372939932, 1393534700, 1587094282, 52859, "SRX22683820", "SRS19677534", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.94807, 0.95298, 0.05682, 0.05385, 0.74004, 0.73925, 0.54423, 0.54484, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Gut", "Digestive System"], [29047, "SRR26990800", "SRX22683819", "SRS19677533", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "WT brain 3", "GSM7924152", null, "source name:brain|tissue:brain|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing", "WT brain 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.", "brain", "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\u00ae 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\u00b0C. 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\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:brain|genotype:wildtype|time:50dpf", "GSM7924152", "GSM7924152: WT brain 3; Danio rerio; RNA Seq", "GSM7924152 r1", "GSM7924152", "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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "6_WT_3B_S21_L001_R2_001.fastq.gz 6_WT_3B_S21_L001_R1_001.fastq.gz", "fastq fastq", 4461174200.0, 14772100.0, "GSM7924152 r1", "0:151 1:151", "A:1278513355;C:956242646;G:972856171;T:1253520960;N:41068", 151, 151, null, null, 1278513355, 956242646, 972856171, 1253520960, 41068, "SRX22683819", "SRS19677533", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.93808, 0.93817, 0.14984, 0.14408, 0.70388, 0.7035, 0.49899, 0.49333, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29048, "SRR26990801", "SRX22683818", "SRS19677532", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "WT brain 2", "GSM7924151", null, "source name:brain|tissue:brain|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing", "WT brain 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.", "brain", "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\u00ae 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\u00b0C. 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\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:brain|genotype:wildtype|time:50dpf", "GSM7924151", "GSM7924151: WT brain 2; Danio rerio; RNA Seq", "GSM7924151 r1", "GSM7924151", "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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "5_WT_2B_S20_L001_R2_001.fastq.gz 5_WT_2B_S20_L001_R1_001.fastq.gz", "fastq fastq", 4801957946.0, 15900523.0, "GSM7924151 r1", "0:151 1:151", "A:1362644269;C:1038749357;G:1059777543;T:1340744881;N:41896", 151, 151, null, null, 1362644269, 1038749357, 1059777543, 1340744881, 41896, "SRX22683818", "SRS19677532", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.9395, 0.94022, 0.14136, 0.13794, 0.70853, 0.70845, 0.48158, 0.51366, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29049, "SRR26990802", "SRX22683817", "SRS19677531", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "WT brain 1", "GSM7924150", null, "source name:brain|tissue:brain|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing", "WT brain 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.", "brain", "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\u00ae 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\u00b0C. 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\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:brain|genotype:wildtype|time:50dpf", "GSM7924150", "GSM7924150: WT brain 1; Danio rerio; RNA Seq", "GSM7924150 r1", "GSM7924150", "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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "4_WT_1B_S19_L001_R1_001.fastq.gz 4_WT_1B_S19_L001_R2_001.fastq.gz", "fastq fastq", 1712568916.0, 5670758.0, "GSM7924150 r1", "0:151 1:151", "A:496576572;C:361494257;G:367701092;T:486774148;N:22847", 151, 151, null, null, 496576572, 361494257, 367701092, 486774148, 22847, "SRX22683817", "SRS19677531", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.92654, 0.92757, 0.14818, 0.14172, 0.71394, 0.7122, 0.5011, 0.50084, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29050, "SRR26990803", "SRX22683816", "SRS19677530", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "itgavKO brain 3", "GSM7924149", null, "source name:brain|tissue:brain|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing", "itgavKO brain 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.", "brain", "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\u00ae 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\u00b0C. 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\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:brain|genotype:itgavKO mutant|time:50dpf", "GSM7924149", "GSM7924149: itgavKO brain 3; Danio rerio; RNA Seq", "GSM7924149 r1", "GSM7924149", "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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "3_itgavKO_3B_S18_L001_R2_001.fastq.gz 3_itgavKO_3B_S18_L001_R1_001.fastq.gz", "fastq fastq", 3079420614.0, 10196757.0, "GSM7924149 r1", "0:151 1:151", "A:869781292;C:673463468;G:684386550;T:851761331;N:27973", 151, 151, null, null, 869781292, 673463468, 684386550, 851761331, 27973, "SRX22683816", "SRS19677530", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.94057, 0.94157, 0.13371, 0.12847, 0.70429, 0.70451, 0.49726, 0.49861, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29051, "SRR26990804", "SRX22683815", "SRS19677529", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "itgavKO brain 2", "GSM7924148", null, "source name:brain|tissue:brain|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing", "itgavKO brain 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.", "brain", "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\u00ae 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\u00b0C. 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\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:brain|genotype:itgavKO mutant|time:50dpf", "GSM7924148", "GSM7924148: itgavKO brain 2; Danio rerio; RNA Seq", "GSM7924148 r1", "GSM7924148", "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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "2_itgavKO_2B_S17_L001_R1_001.fastq.gz 2_itgavKO_2B_S17_L001_R2_001.fastq.gz", "fastq fastq", 1913701218.0, 6336759.0, "GSM7924148 r1", "0:151 1:151", "A:549324781;C:410519448;G:417112515;T:536726028;N:18446", 151, 151, null, null, 549324781, 410519448, 417112515, 536726028, 18446, "SRX22683815", "SRS19677529", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.93075, 0.93209, 0.15174, 0.14613, 0.70449, 0.70475, 0.48199, 0.48317, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29052, "SRR26990805", "SRX22683814", "SRS19677528", "SRP474986", "PRJNA1046526", "ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease", "GSE248975", "Transcriptome Analysis", "Integrin alpha\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "itgavKO brain 1", "GSM7924147", null, "source name:brain|tissue:brain|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing", "itgavKO brain 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.", "brain", "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\u00ae 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\u00b0C. 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\u00b0C and the lighting conditions are 14:10 hr light: dark.", "tissue:brain|genotype:itgavKO mutant|time:50dpf", "GSM7924147", "GSM7924147: itgavKO brain 1; Danio rerio; RNA Seq", "GSM7924147 r1", "GSM7924147", "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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "loader:fastq load.py", "1_itgavKO_1B_S16_L001_R1_001.fastq.gz 1_itgavKO_1B_S16_L001_R2_001.fastq.gz", "fastq fastq", 2056389876.0, 6809238.0, "GSM7924147 r1", "0:151 1:151", "A:593258034;C:437927433;G:446814957;T:578370581;N:18871", 151, 151, null, null, 593258034, 437927433, 446814957, 578370581, 18871, "SRX22683814", "SRS19677528", "SRA1760061", "Muise Lab, Cell Biology, The Hospital for Sick Children", "Muise Lab, Cell Biology, The Hospital for Sick Children", 2, 0.93156, 0.93304, 0.1488, 0.14352, 0.70224, 0.70293, 0.49609, 0.49296, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [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\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "zebrafish itgavko tc 8d 3", "GSM7924146", null, "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\u00ae 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\u00b0C. 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\u00b0C 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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "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, null, null, 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", null, "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\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "zebrafish itgavko tc 8d 2", "GSM7924145", null, "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\u00ae 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\u00b0C. 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\u00b0C 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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "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, null, null, 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", null, "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\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "zebrafish itgavko tc 8d 1", "GSM7924144", null, "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\u00ae 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\u00b0C. 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\u00b0C 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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "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, null, null, 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", null, "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\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "zebrafish wt tc 8d 3", "GSM7924143", null, "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\u00ae 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\u00b0C. 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\u00b0C 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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "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, null, null, 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", null, "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\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "zebrafish wt tc 8d 2", "GSM7924142", null, "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\u00ae 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\u00b0C. 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\u00b0C 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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "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, null, null, 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", null, "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\u2013V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor \u00df TGF \u00df 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 \u00df 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.", null, "pubmed:39526957", null, "zebrafish wt tc 8d 1", "GSM7924141", null, "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\u00ae 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\u00b0C. 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\u00b0C 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\u00ae Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP474986", null, "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, null, null, 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", null, "Canada", "2023-11-29", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [29059, "SRR27010032", "SRX22702842", "SRS19695451", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 scr sham C3", "C3", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:C3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "C3", "C3", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "C3_R2_001.fastq.gz C3_R1_001.fastq.gz", "fastq fastq", 7226125500.0, 24087085.0, "C3 R1 001.fastq.gz", "0:150 1:150", "A:1960622478;C:1648410555;G:1694156766;T:1922924543;N:11158", 150, 150, null, null, 1960622478, 1648410555, 1694156766, 1922924543, 11158, "SRX22702842", "SRS19695451", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94281, 0.94259, 0.11548, 0.11243, 0.666, 0.66768, 0.4931, 0.49197, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29060, "SRR27010033", "SRX22702841", "SRS19695450", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 scr sham C2", "C2", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:C2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "C2", "C2", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "C2_R1_001.fastq.gz C2_R2_001.fastq.gz", "fastq fastq", 5174981700.0, 17249939.0, "C2 R1 001.fastq.gz", "0:150 1:150", "A:1397754308;C:1184093732;G:1220417954;T:1372707855;N:7851", 150, 150, null, null, 1397754308, 1184093732, 1220417954, 1372707855, 7851, "SRX22702841", "SRS19695450", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94447, 0.94375, 0.11969, 0.11666, 0.68885, 0.68956, 0.49127, 0.48884, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29061, "SRR27010034", "SRX22702840", "SRS19695449", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "WT irf8 sham B6", "B6", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:B6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "B6", "B6", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "B6_R1_001.fastq.gz B6_R2_001.fastq.gz", "fastq fastq", 6038798100.0, 20129327.0, "B6 R1 001.fastq.gz", "0:150 1:150", "A:1644314055;C:1369774666;G:1410590989;T:1614109292;N:9098", 150, 150, null, null, 1644314055, 1369774666, 1410590989, 1614109292, 9098, "SRX22702840", "SRS19695449", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94338, 0.9424, 0.12398, 0.12103, 0.69075, 0.69203, 0.49627, 0.49707, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29062, "SRR27010035", "SRX22702839", "SRS19695448", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "WT irf8 sham B4", "B4", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:B4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "B4", "B4", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "B4_R1_001.fastq.gz B4_R2_001.fastq.gz", "fastq fastq", 4670850600.0, 15569502.0, "B4 R1 001.fastq.gz", "0:150 1:150", "A:1265811314;C:1065724201;G:1097798356;T:1241510089;N:6640", 150, 150, null, null, 1265811314, 1065724201, 1097798356, 1241510089, 6640, "SRX22702839", "SRS19695448", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94547, 0.94517, 0.11922, 0.11549, 0.68968, 0.69029, 0.48585, 0.48669, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29063, "SRR27010036", "SRX22702838", "SRS19695446", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "WT irf8 sham B3", "B3", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:B3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "B3", "B3", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "B3_R1_001.fastq.gz B3_R2_001.fastq.gz", "fastq fastq", 5982538500.0, 19941795.0, "B3 R1 001.fastq.gz", "0:150 1:150", "A:1606272011;C:1379162914;G:1419047430;T:1578047050;N:9095", 150, 150, null, null, 1606272011, 1379162914, 1419047430, 1578047050, 9095, "SRX22702838", "SRS19695446", "SRA1760882", "University of York|Biology", "University of York", 2, 0.95017, 0.9501, 0.09939, 0.09688, 0.68838, 0.68964, 0.48756, 0.49223, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29064, "SRR27010037", "SRX22702837", "SRS19695447", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "WT irf8 sham B2", "B2", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:B2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "B2", "B2", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "B2_R2_001.fastq.gz B2_R1_001.fastq.gz", "fastq fastq", 5653227300.0, 18844091.0, "B2 R1 001.fastq.gz", "0:150 1:150", "A:1525579353;C:1295599509;G:1332714404;T:1499325712;N:8322", 150, 150, null, null, 1525579353, 1295599509, 1332714404, 1499325712, 8322, "SRX22702837", "SRS19695447", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94379, 0.89488, 0.12085, 0.10989, 0.69004, 0.69796, 0.48877, 0.48916, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29065, "SRR27010038", "SRX22702836", "SRS19695445", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "WT scr sham A9", "A9", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:A9|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "A9", "A9", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "A9_R1_001.fastq.gz A9_R2_001.fastq.gz", "fastq fastq", 5280286800.0, 17600956.0, "A9 R1 001.fastq.gz", "0:150 1:150", "A:1438789477;C:1200820278;G:1228527888;T:1412141110;N:8047", 150, 150, null, null, 1438789477, 1200820278, 1228527888, 1412141110, 8047, "SRX22702836", "SRS19695445", "SRA1760882", "University of York|Biology", "University of York", 2, 0.93991, 0.93997, 0.12415, 0.11988, 0.68043, 0.68245, 0.49031, 0.49263, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29066, "SRR27010039", "SRX22702835", "SRS19695444", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 irf8 transplanted visible cells G8", "G8", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:G8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "G8", "G8", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "G8_R1_001.fastq.gz G8_R2_001.fastq.gz", "fastq fastq", 6258269400.0, 20860898.0, "G8 R1 001.fastq.gz", "0:150 1:150", "A:1703536007;C:1424705894;G:1461517358;T:1668500971;N:9170", 150, 150, null, null, 1703536007, 1424705894, 1461517358, 1668500971, 9170, "SRX22702835", "SRS19695444", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94463, 0.94425, 0.12179, 0.11924, 0.68383, 0.68574, 0.48927, 0.49078, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29067, "SRR27010040", "SRX22702834", "SRS19695443", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 irf8 transplanted visible cells G5", "G5", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:G5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "G5", "G5", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "G5_R2_001.fastq.gz G5_R1_001.fastq.gz", "fastq fastq", 8086012500.0, 26953375.0, "G5 R1 001.fastq.gz", "0:150 1:150", "A:2209424775;C:1827141351;G:1886144200;T:2163290263;N:11911", 150, 150, null, null, 2209424775, 1827141351, 1886144200, 2163290263, 11911, "SRX22702834", "SRS19695443", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94005, 0.94009, 0.13869, 0.13535, 0.68874, 0.68876, 0.49518, 0.49562, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29068, "SRR27010041", "SRX22702833", "SRS19695442", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 irf8 transplanted visible cells G4", "G4", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:G4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "G4", "G4", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "G4_R2_001.fastq.gz G4_R1_001.fastq.gz", "fastq fastq", 11168836800.0, 37229456.0, "G4 R1 001.fastq.gz", "0:150 1:150", "A:3056935929;C:2522420915;G:2603785258;T:2985677785;N:16913", 150, 150, null, null, 3056935929, 2522420915, 2603785258, 2985677785, 16913, "SRX22702833", "SRS19695442", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94154, 0.94245, 0.13303, 0.12991, 0.68298, 0.68428, 0.49109, 0.49258, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29069, "SRR27010042", "SRX22702832", "SRS19695441", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 irf8 transplanted visible cells G1", "G1", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:G1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "G1", "G1", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "G1_R1_001.fastq.gz G1_R2_001.fastq.gz", "fastq fastq", 6745303500.0, 22484345.0, "G1 R1 001.fastq.gz", "0:150 1:150", "A:1832990297;C:1535916761;G:1572331210;T:1804054965;N:10267", 150, 150, null, null, 1832990297, 1535916761, 1572331210, 1804054965, 10267, "SRX22702832", "SRS19695441", "SRA1760882", "University of York|Biology", "University of York", 2, 0.9424, 0.94298, 0.12822, 0.12534, 0.68775, 0.68854, 0.4869, 0.48958, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29070, "SRR27010043", "SRX22702831", "SRS19695440", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 scr transplanted non visible cells F5", "F5", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:F5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "F5", "F5", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "F5_R1_001.fastq.gz F5_R2_001.fastq.gz", "fastq fastq", 6464113800.0, 21547046.0, "F5 R1 001.fastq.gz", "0:150 1:150", "A:1773652408;C:1452872569;G:1501709404;T:1735869784;N:9635", 150, 150, null, null, 1773652408, 1452872569, 1501709404, 1735869784, 9635, "SRX22702831", "SRS19695440", "SRA1760882", "University of York|Biology", "University of York", 2, 0.93953, 0.93885, 0.13889, 0.13589, 0.68448, 0.68568, 0.49419, 0.49486, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29071, "SRR27010044", "SRX22702830", "SRS19695439", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 scr transplanted non visible cells F4", "F4", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:F4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "F4", "F4", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "F4_R1_001.fastq.gz F4_R2_001.fastq.gz", "fastq fastq", 7547491800.0, 25158306.0, "F4 R1 001.fastq.gz", "0:150 1:150", "A:2043215956;C:1726123019;G:1778767478;T:1999373636;N:11711", 150, 150, null, null, 2043215956, 1726123019, 1778767478, 1999373636, 11711, "SRX22702830", "SRS19695439", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94829, 0.94765, 0.11775, 0.11477, 0.68682, 0.68783, 0.48624, 0.49294, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29072, "SRR27010045", "SRX22702829", "SRS19695437", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 scr transplanted non visible cells F3", "F3", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:F3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "F3", "F3", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "F3_R1_001.fastq.gz F3_R2_001.fastq.gz", "fastq fastq", 7796779800.0, 25989266.0, "F3 R1 001.fastq.gz", "0:150 1:150", "A:2138759764;C:1759352855;G:1808448742;T:2090206548;N:11891", 150, 150, null, null, 2138759764, 1759352855, 1808448742, 2090206548, 11891, "SRX22702829", "SRS19695437", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94125, 0.9421, 0.13575, 0.13224, 0.69307, 0.69469, 0.4862, 0.48802, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29073, "SRR27010046", "SRX22702828", "SRS19695438", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "WT scr sham A4", "A4", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:A4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "A4", "A4", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "A4_R1_001.fastq.gz A4_R2_001.fastq.gz", "fastq fastq", 6954570300.0, 23181901.0, "A4 R1 001.fastq.gz", "0:150 1:150", "A:1888329109;C:1587042583;G:1627429667;T:1851758485;N:10456", 150, 150, null, null, 1888329109, 1587042583, 1627429667, 1851758485, 10456, "SRX22702828", "SRS19695438", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94568, 0.94593, 0.11814, 0.1154, 0.69171, 0.69161, 0.49417, 0.49201, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29074, "SRR27010047", "SRX22702827", "SRS19695436", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 scr transplanted non visible cells F2", "F2", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:F2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "F2", "F2", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "F2_R2_001.fastq.gz F2_R1_001.fastq.gz", "fastq fastq", 7064875200.0, 23549584.0, "F2 R1 001.fastq.gz", "0:150 1:150", "A:1909747576;C:1617295332;G:1667877510;T:1869944260;N:10522", 150, 150, null, null, 1909747576, 1617295332, 1667877510, 1869944260, 10522, "SRX22702827", "SRS19695436", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94737, 0.94827, 0.10024, 0.09772, 0.69057, 0.69146, 0.49402, 0.49924, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29075, "SRR27010048", "SRX22702826", "SRS19695435", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 scr transplanted visible cells E5", "E5", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:E5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "E5", "E5", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "E5_R1_001.fastq.gz E5_R2_001.fastq.gz", "fastq fastq", 9245045700.0, 30816819.0, "E5 R1 001.fastq.gz", "0:150 1:150", "A:2541240585;C:2078884464;G:2136224399;T:2488682323;N:13929", 150, 150, null, null, 2541240585, 2078884464, 2136224399, 2488682323, 13929, "SRX22702826", "SRS19695435", "SRA1760882", "University of York|Biology", "University of York", 2, 0.93981, 0.93963, 0.14018, 0.13679, 0.68544, 0.68647, 0.48749, 0.49123, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29076, "SRR27010049", "SRX22702825", "SRS19695434", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 scr transplanted visible cells E4", "E4", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:E4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "E4", "E4", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "E4_R1_001.fastq.gz E4_R2_001.fastq.gz", "fastq fastq", 9413066700.0, 31376889.0, "E4 R1 001.fastq.gz", "0:150 1:150", "A:2556541599;C:2141951710;G:2209637678;T:2504921319;N:14394", 150, 150, null, null, 2556541599, 2141951710, 2209637678, 2504921319, 14394, "SRX22702825", "SRS19695434", "SRA1760882", "University of York|Biology", "University of York", 2, 0.93966, 0.94056, 0.13191, 0.13025, 0.6845, 0.68458, 0.48562, 0.48775, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29077, "SRR27010050", "SRX22702824", "SRS19695433", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 scr transplanted visible cells E3", "E3", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:E3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "E3", "E3", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "E3_R1_001.fastq.gz E3_R2_001.fastq.gz", "fastq fastq", 7964919000.0, 26549730.0, "E3 R1 001.fastq.gz", "0:150 1:150", "A:2160541660;C:1817481684;G:1869600595;T:2117282750;N:12311", 150, 150, null, null, 2160541660, 1817481684, 1869600595, 2117282750, 12311, "SRX22702824", "SRS19695433", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94418, 0.94436, 0.12381, 0.12155, 0.69043, 0.69244, 0.49578, 0.49427, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29078, "SRR27010051", "SRX22702823", "SRS19695432", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 irf8 sham D7", "D7", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:D7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "D7", "D7", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "D7_R1_001.fastq.gz D7_R2_001.fastq.gz", "fastq fastq", 9187165200.0, 30623884.0, "D7 R1 001.fastq.gz", "0:150 1:150", "A:2491532789;C:2097618431;G:2151100077;T:2446900236;N:13667", 150, 150, null, null, 2491532789, 2097618431, 2151100077, 2446900236, 13667, "SRX22702823", "SRS19695432", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94299, 0.94212, 0.11906, 0.11545, 0.68306, 0.68548, 0.49177, 0.49121, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29079, "SRR27010052", "SRX22702822", "SRS19695430", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 irf8 sham D6", "D6", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:D6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "D6", "D6", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "D6_R1_001.fastq.gz D6_R2_001.fastq.gz", "fastq fastq", 5879800500.0, 19599335.0, "D6 R1 001.fastq.gz", "0:150 1:150", "A:1605109827;C:1329412433;G:1368575434;T:1576693845;N:8961", 150, 150, null, null, 1605109827, 1329412433, 1368575434, 1576693845, 8961, "SRX22702822", "SRS19695430", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94062, 0.94076, 0.12643, 0.12267, 0.67959, 0.68079, 0.4953, 0.49028, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29080, "SRR27010053", "SRX22702821", "SRS19695431", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 irf8 sham D5", "D5", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:D5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "D5", "D5", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "D5_R1_001.fastq.gz D5_R2_001.fastq.gz", "fastq fastq", 6561881400.0, 21872938.0, "D5 R1 001.fastq.gz", "0:150 1:150", "A:1784761040;C:1494553700;G:1531680450;T:1750875924;N:10286", 150, 150, null, null, 1784761040, 1494553700, 1531680450, 1750875924, 10286, "SRX22702821", "SRS19695431", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94309, 0.94372, 0.12249, 0.11939, 0.6896, 0.69126, 0.4916, 0.48496, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29081, "SRR27010054", "SRX22702820", "SRS19695429", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 irf8 sham D2", "D2", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:D2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "D2", "D2", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "D2_R1_001.fastq.gz D2_R2_001.fastq.gz", "fastq fastq", 6654501900.0, 22181673.0, "D2 R1 001.fastq.gz", "0:150 1:150", "A:1814773421;C:1511191953;G:1552895235;T:1775631113;N:10178", 150, 150, null, null, 1814773421, 1511191953, 1552895235, 1775631113, 10178, "SRX22702820", "SRS19695429", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94117, 0.94183, 0.13042, 0.12757, 0.68578, 0.68747, 0.49634, 0.49724, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29082, "SRR27010055", "SRX22702819", "SRS19695428", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 scr sham C5", "C5", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:C5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "C5", "C5", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "C5_R2_001.fastq.gz C5_R1_001.fastq.gz", "fastq fastq", 6839917500.0, 22799725.0, "C5 R1 001.fastq.gz", "0:150 1:150", "A:1862202751;C:1544536021;G:1599909841;T:1833258970;N:9917", 150, 150, null, null, 1862202751, 1544536021, 1599909841, 1833258970, 9917, "SRX22702819", "SRS19695428", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94311, 0.9429, 0.12484, 0.12074, 0.68899, 0.69077, 0.49108, 0.49366, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29083, "SRR27010056", "SRX22702818", "SRS19695427", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "rnaset2 scr sham C4", "C4", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:C4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "C4", "C4", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "C4_R1_001.fastq.gz C4_R2_001.fastq.gz", "fastq fastq", 6814278600.0, 22714262.0, "C4 R1 001.fastq.gz", "0:150 1:150", "A:1829280895;C:1574717969;G:1616401528;T:1793867756;N:10452", 150, 150, null, null, 1829280895, 1574717969, 1616401528, 1793867756, 10452, "SRX22702818", "SRS19695427", "SRA1760882", "University of York|Biology", "University of York", 2, 0.94942, 0.95087, 0.09719, 0.09395, 0.69445, 0.69507, 0.49061, 0.49227, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29084, "SRR27010057", "SRX22702817", "SRS19695425", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "WT scr sham A2", "A2", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:A2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "A2", "A2", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "A2_R1_001.fastq.gz A2_R2_001.fastq.gz", "fastq fastq", 9528853800.0, 31762846.0, "A2 R1 001.fastq.gz", "0:150 1:150", "A:2597197507;C:2160049241;G:2216864264;T:2554728048;N:14740", 150, 150, null, null, 2597197507, 2160049241, 2216864264, 2554728048, 14740, "SRX22702817", "SRS19695425", "SRA1760882", "University of York|Biology", "University of York", 2, 0.9445, 0.94377, 0.12789, 0.12443, 0.68414, 0.68456, 0.48493, 0.49203, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [29085, "SRR27010058", "SRX22702816", "SRS19695426", "SRP475263", "PRJNA1047321", "Effect of microglial replacement on RNAseT2 deficient leukodystrophy in zebrafish", "PRJNA1047321", "Other", "RNA sequencing of zebrafish brains to assess efficiency of macrophage transplantation as a therapy in a zebrafish model of rnaset2 leukodystrophy.", null, null, null, "WT scr sham A1", "A1", null, "strain:nacre|isolate:n/a|breed:n/a|cultivar:n/a|ecotype:n/a|age:4 weeks|dev stage:juvenile|collection date:2023 03|geo loc name:United Kingdom: Sheffield|sex:unknown|tissue:brain|replicate:A1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish: brain", "A1", "A1", "RNA was extracted polyA enriched and libraries prepared with the NEBNext Ultra II Directional RNA Library prep kit for Illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP475263", null, null, "A1_R1_001.fastq.gz A1_R2_001.fastq.gz", "fastq fastq", 7478013000.0, 24926710.0, "A1 R1 001.fastq.gz", "0:150 1:150", "A:2052485809;C:1681219485;G:1732402686;T:2011893634;N:11386", 150, 150, null, null, 2052485809, 1681219485, 1732402686, 2011893634, 11386, "SRX22702816", "SRS19695426", "SRA1760882", "University of York|Biology", "University of York", 2, 0.9395, 0.93867, 0.13153, 0.12753, 0.68933, 0.691, 0.4882, 0.48774, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-12-01", "Multi-stage", "Multi-stage", "Brain", "Nervous System"], [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\u00ae 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.", null, null, null, "smad6ab DKO 5 biol rep 1 5 dpf 5 fish pooled", "GSM8741296", null, "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", null, "For RNA extraction the Rneasy\u00ae 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\u2019 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\u00b0C 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\u00b0C pH 7 5 conductivity 550\u00b5S 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\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "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, null, null, null, 612499747, 307171870, 341630182, 521913046, 316805, "SRX27375433", "SRS23810897", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "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\u00ae 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.", null, null, null, "smad6ab DKO 4 biol rep 1 5 dpf 5 fish pooled", "GSM8741295", null, "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", null, "For RNA extraction the Rneasy\u00ae 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\u2019 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\u00b0C 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\u00b0C pH 7 5 conductivity 550\u00b5S 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\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "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, null, null, null, 610799963, 310255661, 349091544, 536431072, 317485, "SRX27375432", "SRS23810896", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "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\u00ae 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.", null, null, null, "smad6ab DKO 3 biol rep 1 5 dpf 5 fish pooled", "GSM8741294", null, "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", null, "For RNA extraction the Rneasy\u00ae 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\u2019 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\u00b0C 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\u00b0C pH 7 5 conductivity 550\u00b5S 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\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "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, null, null, null, 417424019, 209354549, 238058828, 371172361, 152618, "SRX27375431", "SRS23810895", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "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\u00ae 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.", null, null, null, "smad6ab DKO 2 biol rep 1 5 dpf 5 fish pooled", "GSM8741293", null, "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", null, "For RNA extraction the Rneasy\u00ae 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\u2019 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\u00b0C 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\u00b0C pH 7 5 conductivity 550\u00b5S 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\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "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, null, null, null, 422806413, 210247744, 238495376, 367964420, 207097, "SRX27375430", "SRS23810893", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "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\u00ae 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.", null, null, null, "smad6ab DKO 1 biol rep 1 5 dpf 5 fish pooled", "GSM8741292", null, "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", null, "For RNA extraction the Rneasy\u00ae 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\u2019 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\u00b0C 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\u00b0C pH 7 5 conductivity 550\u00b5S 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\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "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, null, null, null, 600616051, 303681611, 340472236, 526419468, 309434, "SRX27375429", "SRS23810894", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "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\u00ae 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.", null, null, null, "control 5 for smad6abDKO biol rep 1 5 dpf 5 fish pooled", "GSM8741291", null, "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", null, "For RNA extraction the Rneasy\u00ae 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\u2019 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\u00b0C 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\u00b0C pH 7 5 conductivity 550\u00b5S 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\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "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, null, null, null, 544358067, 268587913, 299883067, 461155939, 270039, "SRX27375428", "SRS23810892", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "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\u00ae 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.", null, null, null, "control 4 for smad6abDKO biol rep 1 5 dpf 5 fish pooled", "GSM8741290", null, "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", null, "For RNA extraction the Rneasy\u00ae 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\u2019 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\u00b0C 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\u00b0C pH 7 5 conductivity 550\u00b5S 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\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "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, null, null, null, 413692477, 202818991, 227848971, 353083087, 170274, "SRX27375427", "SRS23810891", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "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\u00ae 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.", null, null, null, "control 3 for smad6abDKO biol rep 1 5 dpf 5 fish pooled", "GSM8741289", null, "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", null, "For RNA extraction the Rneasy\u00ae 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\u2019 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\u00b0C 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\u00b0C pH 7 5 conductivity 550\u00b5S 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\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "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, null, null, null, 493379384, 244908245, 274361129, 420258548, 247444, "SRX27375426", "SRS23810890", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 2375, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"devstage_curation_coarse\" = :p0 order by rowid limit 101", "params": {"p0": "Multi-stage"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 2289, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 40, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_strategy=miRNA-Seq", "selected": false}, {"value": "WGS", "label": "WGS", "count": 24, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_strategy=WGS", "selected": false}, {"value": "RIP-Seq", "label": "RIP-Seq", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_strategy=RIP-Seq", "selected": false}, {"value": "ncRNA-Seq", "label": "ncRNA-Seq", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_strategy=ncRNA-Seq", "selected": false}, {"value": "OTHER", "label": "OTHER", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_strategy=OTHER", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 2302, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_source=TRANSCRIPTOMIC", "selected": false}, {"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 61, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "selected": false}, {"value": "METATRANSCRIPTOMIC", "label": "METATRANSCRIPTOMIC", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_source=METATRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage", "results": [{"value": "cDNA", "label": "cDNA", "count": 2185, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_selection=cDNA", "selected": false}, {"value": "size fractionation", "label": "size fractionation", "count": 40, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_selection=size+fractionation", "selected": false}, {"value": "other", "label": "other", "count": 34, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_selection=other", "selected": false}, {"value": "PolyA", "label": "PolyA", "count": 33, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_selection=PolyA", "selected": false}, {"value": "RANDOM", "label": "RANDOM", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_selection=RANDOM", "selected": false}, {"value": "RT-PCR", "label": "RT-PCR", "count": 26, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_selection=RT-PCR", "selected": false}, {"value": "PCR", "label": "PCR", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_selection=PCR", "selected": false}, {"value": "Oligo-dT", "label": "Oligo-dT", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_selection=Oligo-dT", "selected": false}, {"value": "RACE", "label": "RACE", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_selection=RACE", "selected": false}, {"value": "cDNA_oligo_dT", "label": "cDNA_oligo_dT", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_selection=cDNA_oligo_dT", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 1700, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_layout=PAIRED", "selected": false}, {"value": "SINGLE", "label": "SINGLE", "count": 675, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 2215, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.platform=ILLUMINA", "selected": false}, {"value": "BGISEQ", "label": "BGISEQ", "count": 67, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.platform=BGISEQ", "selected": false}, {"value": "DNBSEQ", "label": "DNBSEQ", "count": 57, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.platform=DNBSEQ", "selected": false}, {"value": "ELEMENT", "label": "ELEMENT", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.platform=ELEMENT", "selected": false}, {"value": "ION_TORRENT", "label": "ION_TORRENT", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&experiment.platform=ION_TORRENT", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage", "results": [{"value": "Multi-stage", "label": "Multi-stage", "count": 2375, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json", "selected": true}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage", "results": [{"value": "Multi-stage", "label": "Multi-stage", "count": 2024, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&devstage_curation=Multi-stage", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 351, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&devstage_curation=Undetermined", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 1212, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=All+anatomical+structures", "selected": false}, {"value": "Nervous System", "label": "Nervous System", "count": 277, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Nervous+System", "selected": false}, {"value": "Surface Structure", "label": "Surface Structure", "count": 218, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Surface+Structure", "selected": false}, {"value": "Sensory System", "label": "Sensory System", "count": 143, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Sensory+System", "selected": false}, {"value": "Renal System", "label": "Renal System", "count": 119, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Renal+System", "selected": false}, {"value": "Liver and Biliary System", "label": "Liver and Biliary System", "count": 104, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Liver+and+Biliary+System", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 67, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Undetermined", "selected": false}, {"value": "Cardiovascular System", "label": "Cardiovascular System", "count": 59, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Cardiovascular+System", "selected": false}, {"value": "Skeletal Element", "label": "Skeletal Element", "count": 32, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Skeletal+Element", "selected": false}, {"value": "Muscular System", "label": "Muscular System", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation_coarse=Muscular+System", "selected": false}], "truncated": true}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage", "results": [{"value": "Whole Organism", "label": "Whole Organism", "count": 877, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Whole+Organism", "selected": false}, {"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 335, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Embryo+Imprecise", "selected": false}, {"value": "Brain", "label": "Brain", "count": 243, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Brain", "selected": false}, {"value": "Eye", "label": "Eye", "count": 131, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Eye", "selected": false}, {"value": "Kidney", "label": "Kidney", "count": 119, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Kidney", "selected": false}, {"value": "Trunk", "label": "Trunk", "count": 116, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk", "selected": false}, {"value": "Liver", "label": "Liver", "count": 104, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Liver", "selected": false}, {"value": "Fin", "label": "Fin", "count": 94, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Fin", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 67, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Undetermined", "selected": false}, {"value": "Heart", "label": "Heart", "count": 44, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Heart", "selected": false}], "truncated": true}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage", "results": [{"value": "unknown", "label": "unknown", "count": 1661, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&technology=unknown", "selected": false}, {"value": "bulk", "label": "bulk", "count": 273, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&technology=bulk", "selected": false}, {"value": "scartrace", "label": "scartrace", "count": 171, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&technology=scartrace", "selected": false}, {"value": "smartseq", "label": "smartseq", "count": 97, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&technology=smartseq", "selected": false}, {"value": "10x", "label": "10x", "count": 94, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&technology=10x", "selected": false}, {"value": "microwellseq", "label": "microwellseq", "count": 55, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&technology=microwellseq", "selected": false}, {"value": "generic-scrnaseq-only", "label": "generic-scrnaseq-only", "count": 13, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&technology=generic-scrnaseq-only", "selected": false}, {"value": "celseq", "label": "celseq", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&technology=celseq", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": "29132", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&_next=29132", "private": false, "allow_execute_sql": true, "query_ms": 151.27239800131065}