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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"], [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 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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"], [29133, "SRR32025064", "SRX27375425", "SRS23810888", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\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 2 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled", "GSM8741288", 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 2 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 whole embryos", 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", "GSM8741288", "GSM8741288: control 2 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq", "GSM8741288 r1", "GSM8741288", "1", "For RNA extraction  the Rneasy\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, "22_wt_control_F10_R1.fastq.gz", "fastq", 1283795850.0, 17117278.0, "GSM8741288 r1", "0:75", "A:442456808;C:219464610;G:244269392;T:377385874;N:219166", 75, null, null, null, 442456808, 219464610, 244269392, 377385874, 219166, "SRX27375425", "SRS23810888", "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"], [29134, "SRR32025065", "SRX27375424", "SRS23810889", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\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 1 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled", "GSM8741287", 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 1 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 whole embryos", 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", "GSM8741287", "GSM8741287: control 1 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq", "GSM8741287 r1", "GSM8741287", "1", "For RNA extraction  the Rneasy\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, "21_wt_control_E10_R1.fastq.gz", "fastq", 1620787500.0, 21610500.0, "GSM8741287 r1", "0:75", "A:556979571;C:275622807;G:309210789;T:478725788;N:248545", 75, null, null, null, 556979571, 275622807, 309210789, 478725788, 248545, "SRX27375424", "SRS23810889", "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"], [29135, "SRR32025066", "SRX27375423", "SRS23810887", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\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, "smad3ab DKO 5  biol rep 1  5 dpf  5 fish pooled", "GSM8741286", null, "source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad3a/b DKO|geo loc name:missing|collection date:missing", "smad3ab DKO 5  biol rep 1  5 dpf  5 fish pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 whole embryos", 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:smad3a/b DKO", "GSM8741286", "GSM8741286: smad3ab DKO 5  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq", "GSM8741286 r1", "GSM8741286", "1", "For RNA extraction  the Rneasy\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, "20_smad3a__smad3b__D10_R1.fastq.gz", "fastq", 1664067900.0, 22187572.0, "GSM8741286 r1", "0:75", "A:575504153;C:284148304;G:316755855;T:487400701;N:258887", 75, null, null, null, 575504153, 284148304, 316755855, 487400701, 258887, "SRX27375423", "SRS23810887", "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"], [29136, "SRR32025067", "SRX27375422", "SRS23810886", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\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, "smad3ab DKO 4  biol rep 1  5 dpf  5 fish pooled", "GSM8741285", null, "source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad3a/b DKO|geo loc name:missing|collection date:missing", "smad3ab DKO 4  biol rep 1  5 dpf  5 fish pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 whole embryos", 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:smad3a/b DKO", "GSM8741285", "GSM8741285: smad3ab DKO 4  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq", "GSM8741285 r1", "GSM8741285", "1", "For RNA extraction  the Rneasy\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, "19_smad3a__smad3b__C10_R1.fastq.gz", "fastq", 1277250825.0, 17030011.0, "GSM8741285 r1", "0:75", "A:441711745;C:218346228;G:242350714;T:374666966;N:175172", 75, null, null, null, 441711745, 218346228, 242350714, 374666966, 175172, "SRX27375422", "SRS23810886", "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"], [29137, "SRR32025068", "SRX27375421", "SRS23810885", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\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, "smad3ab DKO 3  biol rep 1  5 dpf  5 fish pooled", "GSM8741284", null, "source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad3a/b DKO|geo loc name:missing|collection date:missing", "smad3ab DKO 3  biol rep 1  5 dpf  5 fish pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 whole embryos", 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:smad3a/b DKO", "GSM8741284", "GSM8741284: smad3ab DKO 3  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq", "GSM8741284 r1", "GSM8741284", "1", "For RNA extraction  the Rneasy\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, "18_smad3a__smad3b__B10_R1.fastq.gz", "fastq", 1564334850.0, 20857798.0, "GSM8741284 r1", "0:75", "A:538189348;C:271673806;G:298029553;T:456167924;N:274219", 75, null, null, null, 538189348, 271673806, 298029553, 456167924, 274219, "SRX27375421", "SRS23810885", "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"], [29138, "SRR32025069", "SRX27375420", "SRS23810883", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\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, "smad3ab DKO 2  biol rep 1  5 dpf  5 fish pooled", "GSM8741283", null, "source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad3a/b DKO|geo loc name:missing|collection date:missing", "smad3ab DKO 2  biol rep 1  5 dpf  5 fish pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 whole embryos", 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:smad3a/b DKO", "GSM8741283", "GSM8741283: smad3ab DKO 2  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq", "GSM8741283 r1", "GSM8741283", "1", "For RNA extraction  the Rneasy\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, "17_smad3a__smad3b__A10_R1.fastq.gz", "fastq", 1496334900.0, 19951132.0, "GSM8741283 r1", "0:75", "A:514961004;C:254586630;G:285562274;T:440963052;N:261940", 75, null, null, null, 514961004, 254586630, 285562274, 440963052, 261940, "SRX27375420", "SRS23810883", "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"], [29139, "SRR32025070", "SRX27375419", "SRS23810884", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\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, "smad3ab DKO 1  biol rep 1  5 dpf  5 fish pooled", "GSM8741282", null, "source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad3a/b DKO|geo loc name:missing|collection date:missing", "smad3ab DKO 1  biol rep 1  5 dpf  5 fish pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 whole embryos", 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:smad3a/b DKO", "GSM8741282", "GSM8741282: smad3ab DKO 1  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq", "GSM8741282 r1", "GSM8741282", "1", "For RNA extraction  the Rneasy\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, "16_smad3a__smad3b__H9_R1.fastq.gz", "fastq", 1403963250.0, 18719510.0, "GSM8741282 r1", "0:75", "A:488946191;C:233615962;G:269240931;T:411958629;N:201537", 75, null, null, null, 488946191, 233615962, 269240931, 411958629, 201537, "SRX27375419", "SRS23810884", "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"], [29140, "SRR32025071", "SRX27375418", "SRS23810882", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\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 smad3abDKO  biol rep 1  5 dpf  5 fish pooled", "GSM8741281", 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 smad3abDKO  biol rep 1  5 dpf  5 fish pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 whole embryos", 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", "GSM8741281", "GSM8741281: control 5 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq", "GSM8741281 r1", "GSM8741281", "1", "For RNA extraction  the Rneasy\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, "15_wt_control_G9_R1.fastq.gz", "fastq", 1565513400.0, 20873512.0, "GSM8741281 r1", "0:75", "A:537915091;C:264328012;G:304123957;T:458903666;N:242674", 75, null, null, null, 537915091, 264328012, 304123957, 458903666, 242674, "SRX27375418", "SRS23810882", "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"], [29141, "SRR32025072", "SRX27375417", "SRS23810881", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\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 smad3abDKO  biol rep 1  5 dpf  5 fish pooled", "GSM8741280", 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 smad3abDKO  biol rep 1  5 dpf  5 fish pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 whole embryos", 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", "GSM8741280", "GSM8741280: control 4 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq", "GSM8741280 r1", "GSM8741280", "1", "For RNA extraction  the Rneasy\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, "14_wt_control_F9_R1.fastq.gz", "fastq", 1289377350.0, 17191698.0, "GSM8741280 r1", "0:75", "A:444884871;C:212056955;G:249450087;T:382793805;N:191632", 75, null, null, null, 444884871, 212056955, 249450087, 382793805, 191632, "SRX27375417", "SRS23810881", "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"], [29142, "SRR32025073", "SRX27375416", "SRS23810880", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\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 smad3abDKO  biol rep 1  5 dpf  5 fish pooled", "GSM8741279", 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 smad3abDKO  biol rep 1  5 dpf  5 fish pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 whole embryos", 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", "GSM8741279", "GSM8741279: control 3 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq", "GSM8741279 r1", "GSM8741279", "1", "For RNA extraction  the Rneasy\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, "13_wt_control_E9_R1.fastq.gz", "fastq", 1500149700.0, 20001996.0, "GSM8741279 r1", "0:75", "A:516842151;C:249094684;G:289026249;T:444994403;N:192213", 75, null, null, null, 516842151, 249094684, 289026249, 444994403, 192213, "SRX27375416", "SRS23810880", "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"], [29143, "SRR32025074", "SRX27375415", "SRS23810879", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\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 2 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled", "GSM8741278", 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 2 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 whole embryos", 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", "GSM8741278", "GSM8741278: control 2 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq", "GSM8741278 r1", "GSM8741278", "1", "For RNA extraction  the Rneasy\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, "12_wt_control_D9_R1.fastq.gz", "fastq", 1826731050.0, 24356414.0, "GSM8741278 r1", "0:75", "A:624589544;C:306590828;G:354308807;T:540924959;N:316912", 75, null, null, null, 624589544, 306590828, 354308807, 540924959, 316912, "SRX27375415", "SRS23810879", "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"], [29144, "SRR32025075", "SRX27375414", "SRS23810878", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\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 1 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled", "GSM8741277", 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 1 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 whole embryos", 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", "GSM8741277", "GSM8741277: control 1 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq", "GSM8741277 r1", "GSM8741277", "1", "For RNA extraction  the Rneasy\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, "11_wt_control_C9_R1.fastq.gz", "fastq", 1657528425.0, 22100379.0, "GSM8741277 r1", "0:75", "A:567762447;C:276623380;G:320467937;T:492394510;N:280151", 75, null, null, null, 567762447, 276623380, 320467937, 492394510, 280151, "SRX27375414", "SRS23810878", "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"], [29145, "SRR32025076", "SRX27375413", "SRS23810876", "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, "qKO 5  biol rep 1  adult aorta  3 aortas pooled", "GSM8741276", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 5  biol rep 1  adult aorta  3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741276", "GSM8741276: qKO 5  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741276 r1", "GSM8741276", "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, "10_qKO_B9_R1.fastq.gz", "fastq", 1749103950.0, 23321386.0, "GSM8741276 r1", "0:75", "A:608737363;C:302455983;G:338119173;T:499492171;N:299260", 75, null, null, null, 608737363, 302455983, 338119173, 499492171, 299260, "SRX27375413", "SRS23810876", "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", "Heart", "Cardiovascular System"], [29146, "SRR32025077", "SRX27375412", "SRS23810877", "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, "qKO 4  biol rep 1  adult aorta  3 aortas pooled", "GSM8741275", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 4  biol rep 1  adult aorta  3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741275", "GSM8741275: qKO 4  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741275 r1", "GSM8741275", "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, "9_qKO_A9_R1.fastq.gz", "fastq", 1391151150.0, 18548682.0, "GSM8741275 r1", "0:75", "A:493715157;C:235480005;G:265878909;T:395857913;N:219166", 75, null, null, null, 493715157, 235480005, 265878909, 395857913, 219166, "SRX27375412", "SRS23810877", "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", "Heart", "Cardiovascular System"], [29147, "SRR32025078", "SRX27375411", "SRS23810875", "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, "qKO 3  biol rep 1  adult aorta  3 aortas pooled", "GSM8741274", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 3  biol rep 1  adult aorta  3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741274", "GSM8741274: qKO 3  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741274 r1", "GSM8741274", "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, "8_qKO_H8_R1.fastq.gz", "fastq", 1548693000.0, 20649240.0, "GSM8741274 r1", "0:75", "A:546086416;C:265907989;G:302995102;T:433434795;N:268698", 75, null, null, null, 546086416, 265907989, 302995102, 433434795, 268698, "SRX27375411", "SRS23810875", "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", "Heart", "Cardiovascular System"], [29148, "SRR32025079", "SRX27375410", "SRS23810873", "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, "qKO 2  biol rep 1  adult aorta  3 aortas pooled", "GSM8741273", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 2  biol rep 1  adult aorta  3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741273", "GSM8741273: qKO 2  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741273 r1", "GSM8741273", "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, "7_qKO_G8_R1.fastq.gz", "fastq", 1420837575.0, 18944501.0, "GSM8741273 r1", "0:75", "A:505066296;C:237130175;G:277345211;T:401058536;N:237357", 75, null, null, null, 505066296, 237130175, 277345211, 401058536, 237357, "SRX27375410", "SRS23810873", "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", "Heart", "Cardiovascular System"], [29149, "SRR32025080", "SRX27375409", "SRS23810874", "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, "qKO 1  biol rep 1  adult aorta  3 aortas pooled", "GSM8741272", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 1  biol rep 1  adult aorta  3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741272", "GSM8741272: qKO 1  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741272 r1", "GSM8741272", "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, "6_qKO_F8_R1.fastq.gz", "fastq", 1486031025.0, 19813747.0, "GSM8741272 r1", "0:75", "A:520876345;C:250796628;G:293184034;T:420907913;N:266105", 75, null, null, null, 520876345, 250796628, 293184034, 420907913, 266105, "SRX27375409", "SRS23810874", "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", "Heart", "Cardiovascular System"], [29150, "SRR32025081", "SRX27375408", "SRS23810872", "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  biol rep 1  adult aorta  3 aortas pooled", "GSM8741271", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 5  biol rep 1  adult aorta  3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741271", "GSM8741271: control 5  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741271 r1", "GSM8741271", "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, "5_wt_control_E8_R1.fastq.gz", "fastq", 1415975175.0, 18879669.0, "GSM8741271 r1", "0:75", "A:499498659;C:237283969;G:278581269;T:400389063;N:222215", 75, null, null, null, 499498659, 237283969, 278581269, 400389063, 222215, "SRX27375408", "SRS23810872", "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", "Heart", "Cardiovascular System"], [29151, "SRR32025082", "SRX27375407", "SRS23810871", "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  biol rep 1  adult aorta  3 aortas pooled", "GSM8741270", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 4  biol rep 1  adult aorta  3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741270", "GSM8741270: control 4  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741270 r1", "GSM8741270", "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, "4_wt_control_D8_R1.fastq.gz", "fastq", 1448565375.0, 19314205.0, "GSM8741270 r1", "0:75", "A:515361139;C:240035739;G:286658162;T:406262131;N:248204", 75, null, null, null, 515361139, 240035739, 286658162, 406262131, 248204, "SRX27375407", "SRS23810871", "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", "Heart", "Cardiovascular System"], [29152, "SRR32025083", "SRX27375406", "SRS23810870", "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  biol rep 1  adult aorta  3 aortas pooled", "GSM8741269", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 3  biol rep 1  adult aorta  3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741269", "GSM8741269: control 3  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741269 r1", "GSM8741269", "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, "3_wt_control_C8_R1.fastq.gz", "fastq", 1171513275.0, 15620177.0, "GSM8741269 r1", "0:75", "A:417371801;C:198042286;G:227929434;T:328006138;N:163616", 75, null, null, null, 417371801, 198042286, 227929434, 328006138, 163616, "SRX27375406", "SRS23810870", "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", "Heart", "Cardiovascular System"], [29153, "SRR32025084", "SRX27375405", "SRS23810869", "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 2  biol rep 1  adult aorta  3 aortas pooled", "GSM8741268", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 2  biol rep 1  adult aorta  3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741268", "GSM8741268: control 2  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741268 r1", "GSM8741268", "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, "2_wt_control_B8_R1.fastq.gz", "fastq", 1379973000.0, 18399640.0, "GSM8741268 r1", "0:75", "A:487735196;C:232122567;G:270442978;T:389464154;N:208105", 75, null, null, null, 487735196, 232122567, 270442978, 389464154, 208105, "SRX27375405", "SRS23810869", "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", "Heart", "Cardiovascular System"], [29154, "SRR32025085", "SRX27375404", "SRS23810868", "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 1  biol rep 1  adult aorta  3 aortas pooled", "GSM8741267", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 1  biol rep 1  adult aorta  3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741267", "GSM8741267: control 1  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741267 r1", "GSM8741267", "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, "1_wt_control_A8_R1.fastq.gz", "fastq", 1068193125.0, 14242575.0, "GSM8741267 r1", "0:75", "A:379776425;C:179521683;G:209337737;T:299415096;N:142184", 75, null, null, null, 379776425, 179521683, 209337737, 299415096, 142184, "SRX27375404", "SRS23810868", "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", "Heart", "Cardiovascular System"], [29175, "SRR27292304", "SRX22969963", "SRS19936063", "SRP479046", "PRJNA1054617", "Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish", "GSE250610", "Transcriptome Analysis", "Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5\u00b0C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 \u00b0C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.", null, "pubmed:38922186", null, "Burned Larval Zebrafish  48 hours post burn", "GSM7982886", null, "source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing", "Burned Larval Zebrafish  48 hours post burn", "FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix", "Whole blood", "Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.", "Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing", "Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5\u02daC incubator.", "tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn", "GSM7982886", "GSM7982886: Burned Larval Zebrafish  48 hours post burn; Danio rerio; RNA Seq", "GSM7982886 r1", "GSM7982886", "1", "Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP479046", null, "loader:fastq load.py", "Burn-48hpb_S5_L001_R2_001.fastq.gz Burn-48hpb_S5_L001_R1_001.fastq.gz", "fastq fastq", 20874980529.0, 178418637.0, "GSM7982886 r1", "0:28 1:89", "A:5945091269;C:4392590896;G:4497688824;T:6035946283;N:3663257", 28, 89, null, null, 5945091269, 4392590896, 4497688824, 6035946283, 3663257, "SRX22969963", "SRS19936063", "SRA1772557", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 2, 0.00573, 0.91666, 0.00222, 0.19474, 0.9931, 0.79306, 0.42082, 0.53801, 28, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-12-19", "Multi-stage", "Multi-stage", "Blood", "Hematopoietic System"], [29176, "SRR27292305", "SRX22969963", "SRS19936063", "SRP479046", "PRJNA1054617", "Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish", "GSE250610", "Transcriptome Analysis", "Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5\u00b0C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 \u00b0C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.", null, "pubmed:38922186", null, "Burned Larval Zebrafish  48 hours post burn", "GSM7982886", null, "source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing", "Burned Larval Zebrafish  48 hours post burn", "FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix", "Whole blood", "Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.", "Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing", "Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5\u02daC incubator.", "tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn", "GSM7982886", "GSM7982886: Burned Larval Zebrafish  48 hours post burn; Danio rerio; RNA Seq", "GSM7982886 r1", "GSM7982886", "1", "Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP479046", null, "loader:fastq load.py", "Burn-48hpb_S5_L002_R1_001.fastq.gz Burn-48hpb_S5_L002_R2_001.fastq.gz", "fastq fastq", 20022973425.0, 171136525.0, "GSM7982886 r2", "0:28 1:89", "A:5709681181;C:4208386174;G:4307510275;T:5796282368;N:1113427", 28, 89, null, null, 5709681181, 4208386174, 4307510275, 5796282368, 1113427, "SRX22969963", "SRS19936063", "SRA1772557", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 2, 0.00547, 0.9154, 0.00202, 0.1955, 0.99283, 0.79423, 0.39307, 0.53427, 28, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-12-19", "Multi-stage", "Multi-stage", "Blood", "Hematopoietic System"], [29177, "SRR27292306", "SRX22969962", "SRS19936064", "SRP479046", "PRJNA1054617", "Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish", "GSE250610", "Transcriptome Analysis", "Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5\u00b0C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 \u00b0C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.", null, "pubmed:38922186", null, "Burned Larval Zebrafish  24 hours post burn", "GSM7982885", null, "source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing", "Burned Larval Zebrafish  24 hours post burn", "FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix", "Whole blood", "Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.", "Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing", "Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5\u02daC incubator.", "tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn", "GSM7982885", "GSM7982885: Burned Larval Zebrafish  24 hours post burn; Danio rerio; RNA Seq", "GSM7982885 r1", "GSM7982885", "1", "Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP479046", null, "loader:fastq load.py", "Burn-24hpb_S2_L001_R1_001.fastq.gz Burn-24hpb_S2_L001_R2_001.fastq.gz", "fastq fastq", 9782870058.0, 83614274.0, "GSM7982885 r1", "0:28 1:89", "A:2744737668;C:2140848416;G:2249400157;T:2645170677;N:2713140", 28, 89, null, null, 2744737668, 2140848416, 2249400157, 2645170677, 2713140, "SRX22969962", "SRS19936064", "SRA1772557", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 2, 0.00752, 0.92059, 0.00244, 0.16143, 0.98944, 0.82929, 0.44176, 0.54525, 28, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-12-19", "Multi-stage", "Multi-stage", "Blood", "Hematopoietic System"], [29178, "SRR27292307", "SRX22969962", "SRS19936064", "SRP479046", "PRJNA1054617", "Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish", "GSE250610", "Transcriptome Analysis", "Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5\u00b0C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 \u00b0C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.", null, "pubmed:38922186", null, "Burned Larval Zebrafish  24 hours post burn", "GSM7982885", null, "source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing", "Burned Larval Zebrafish  24 hours post burn", "FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix", "Whole blood", "Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.", "Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing", "Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5\u02daC incubator.", "tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn", "GSM7982885", "GSM7982885: Burned Larval Zebrafish  24 hours post burn; Danio rerio; RNA Seq", "GSM7982885 r1", "GSM7982885", "1", "Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP479046", null, "loader:fastq load.py", "Burn-24hpb_S2_L002_R2_001.fastq.gz Burn-24hpb_S2_L002_R1_001.fastq.gz", "fastq fastq", 9861989202.0, 84290506.0, "GSM7982885 r2", "0:28 1:89", "A:2769268861;C:2158644227;G:2263475493;T:2669311436;N:1289185", 28, 89, null, null, 2769268861, 2158644227, 2263475493, 2669311436, 1289185, "SRX22969962", "SRS19936064", "SRA1772557", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 2, 0.0076, 0.9197, 0.00232, 0.16162, 0.98995, 0.82852, 0.43786, 0.55256, 28, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-12-19", "Multi-stage", "Multi-stage", "Blood", "Hematopoietic System"], [29179, "SRR27292308", "SRX22969961", "SRS19936062", "SRP479046", "PRJNA1054617", "Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish", "GSE250610", "Transcriptome Analysis", "Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5\u00b0C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 \u00b0C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.", null, "pubmed:38922186", null, "Burned Larval Zebrafish  6 hours post burn", "GSM7982884", null, "source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing", "Burned Larval Zebrafish  6 hours post burn", "FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix", "Whole blood", "Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.", "Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing", "Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5\u02daC incubator.", "tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn", "GSM7982884", "GSM7982884: Burned Larval Zebrafish  6 hours post burn; Danio rerio; RNA Seq", "GSM7982884 r1", "GSM7982884", "1", "Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP479046", null, "loader:fastq load.py", "Burn-6hpb_S7_L001_R1_001.fastq.gz Burn-6hpb_S7_L001_R2_001.fastq.gz", "fastq fastq", 12475938384.0, 106631952.0, "GSM7982884 r1", "0:28 1:89", "A:3401989108;C:2878275107;G:3114945415;T:3078525361;N:2203393", 28, 89, null, null, 3401989108, 2878275107, 3114945415, 3078525361, 2203393, "SRX22969961", "SRS19936062", "SRA1772557", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 2, 0.01053, 0.89396, 0.00429, 0.18315, 0.99458, 0.85756, 0.34876, 0.58728, 28, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-12-19", "Multi-stage", "Multi-stage", "Blood", "Hematopoietic System"], [29180, "SRR27292309", "SRX22969961", "SRS19936062", "SRP479046", "PRJNA1054617", "Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish", "GSE250610", "Transcriptome Analysis", "Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5\u00b0C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 \u00b0C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.", null, "pubmed:38922186", null, "Burned Larval Zebrafish  6 hours post burn", "GSM7982884", null, "source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing", "Burned Larval Zebrafish  6 hours post burn", "FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix", "Whole blood", "Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.", "Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing", "Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5\u02daC incubator.", "tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn", "GSM7982884", "GSM7982884: Burned Larval Zebrafish  6 hours post burn; Danio rerio; RNA Seq", "GSM7982884 r1", "GSM7982884", "1", "Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP479046", null, "loader:fastq load.py", "Burn-6hpb_S7_L002_R1_001.fastq.gz Burn-6hpb_S7_L002_R2_001.fastq.gz", "fastq fastq", 11874083247.0, 101487891.0, "GSM7982884 r2", "0:28 1:89", "A:3243501055;C:2735412615;G:2958387721;T:2936117380;N:664476", 28, 89, null, null, 3243501055, 2735412615, 2958387721, 2936117380, 664476, "SRX22969961", "SRS19936062", "SRA1772557", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 2, 0.01063, 0.89389, 0.00439, 0.18047, 0.99403, 0.85878, 0.36393, 0.54831, 28, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-12-19", "Multi-stage", "Multi-stage", "Blood", "Hematopoietic System"], [29181, "SRR27292310", "SRX22969960", "SRS19936061", "SRP479046", "PRJNA1054617", "Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish", "GSE250610", "Transcriptome Analysis", "Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5\u00b0C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 \u00b0C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.", null, "pubmed:38922186", null, "Unwounded Larval Zebrafish  5 dpf", "GSM7982883", null, "source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing", "Unwounded Larval Zebrafish  5 dpf", "FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix", "Whole blood", "Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.", "Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing", "Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5\u02daC incubator.", "tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded", "GSM7982883", "GSM7982883: Unwounded Larval Zebrafish  5 dpf Danio rerio; RNA Seq", "GSM7982883 r1", "GSM7982883", "1", "Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP479046", null, "loader:fastq load.py", "WT-5dpf_S6_L001_R2_001.fastq.gz WT-5dpf_S6_L001_R1_001.fastq.gz", "fastq fastq", 31813158312.0, 271907336.0, "GSM7982883 r1", "0:28 1:89", "A:8991313503;C:6911976524;G:7105775004;T:8798521232;N:5572049", 28, 89, null, null, 8991313503, 6911976524, 7105775004, 8798521232, 5572049, "SRX22969960", "SRS19936061", "SRA1772557", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 2, 0.00661, 0.92343, 0.00245, 0.19293, 0.99255, 0.81379, 0.35935, 0.54818, 28, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-12-19", "Multi-stage", "Multi-stage", "Blood", "Hematopoietic System"], [29182, "SRR27292311", "SRX22969960", "SRS19936061", "SRP479046", "PRJNA1054617", "Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish", "GSE250610", "Transcriptome Analysis", "Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5\u00b0C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 \u00b0C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.", null, "pubmed:38922186", null, "Unwounded Larval Zebrafish  5 dpf", "GSM7982883", null, "source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing", "Unwounded Larval Zebrafish  5 dpf", "FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix", "Whole blood", "Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.", "Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing", "Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5\u02daC incubator.", "tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded", "GSM7982883", "GSM7982883: Unwounded Larval Zebrafish  5 dpf Danio rerio; RNA Seq", "GSM7982883 r1", "GSM7982883", "1", "Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP479046", null, "loader:fastq load.py", "WT-5dpf_S6_L002_R1_001.fastq.gz WT-5dpf_S6_L002_R2_001.fastq.gz", "fastq fastq", 30524386113.0, 260892189.0, "GSM7982883 r2", "0:28 1:89", "A:8637605077;C:6625244702;G:6807369409;T:8452468968;N:1697957", 28, 89, null, null, 8637605077, 6625244702, 6807369409, 8452468968, 1697957, "SRX22969960", "SRS19936061", "SRA1772557", "University of Wisconsin-Madison", "University of Wisconsin-Madison", 2, 0.00648, 0.92418, 0.00233, 0.19549, 0.99241, 0.81444, 0.37733, 0.54674, 28, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-12-19", "Multi-stage", "Multi-stage", "Blood", "Hematopoietic System"]], "truncated": false, "filtered_table_rows_count": 2185, "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", 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