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Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. 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Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. 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Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. 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Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. 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This submission includes reads tagged with the sequence TAGCTT.", "Small RNA miRNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP013615", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16", "18732_1#10.cram", "cram", 263295150.0, 5265903.0, "SC RUN 18732 1#10", "0:50", "A:75332297;C:66059671;G:68562462;T:53315439;N:25281", 50, null, null, null, 75332297, 66059671, 68562462, 53315439, 25281, "ERX1468062", "ERS1051434", "ERA612385", "European Nucleotide Archive", "Wellcome Sanger Institute", 1, 0.61939, null, 0.10112, null, 0.89613, null, 0.55542, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-02-03", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [3054, "ERR1396802", "ERX1468061", "ERS1051433", "ERP013615", "PRJEB12173", "Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts", "Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011", "Transcriptome Analysis", "Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.", "ArrayExpress:E ERAD 449", null, null, "zmp ph229 dicer A10", "SAMEA3864299", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864299|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:26Z|INSDC status:public|Submitter Id:29ffff30 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29ffff30 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "SC EXP 18732 1#9", "15616870", "Illumina sequencing of library 15616870 constructed from sample accession ERS1051433 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GATCAG.", "Small RNA miRNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP013615", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16", "18732_1#9.cram", "cram", 7506900.0, 150138.0, "SC RUN 18732 1#9", "0:50", "A:2194276;C:1883363;G:1959471;T:1468994;N:796", 50, null, null, null, 2194276, 1883363, 1959471, 1468994, 796, "ERX1468061", "ERS1051433", "ERA612385", "European Nucleotide Archive", "Wellcome Sanger Institute", 1, 0.60026, null, 0.10518, null, 0.91106, null, 0.55508, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-02-03", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [3055, "ERR1396801", "ERX1468060", "ERS1051432", "ERP013615", "PRJEB12173", "Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts", "Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011", "Transcriptome Analysis", "Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.", "ArrayExpress:E ERAD 449", null, null, "zmp ph228 drosha C1", "SAMEA3864298", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864298|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:26Z|INSDC status:public|Submitter Id:29f306e0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29f306e0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "SC EXP 18732 1#8", "15616953", "Illumina sequencing of library 15616953 constructed from sample accession ERS1051432 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ACTTGA.", "Small RNA miRNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP013615", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16", "18732_1#8.cram", "cram", 464447300.0, 9288946.0, "SC RUN 18732 1#8", "0:50", "A:136629424;C:120103988;G:117495447;T:90173901;N:44540", 50, null, null, null, 136629424, 120103988, 117495447, 90173901, 44540, "ERX1468060", "ERS1051432", "ERA612385", "European Nucleotide Archive", "Wellcome Sanger Institute", 1, 0.51298, null, 0.10188, null, 0.88434, null, 0.6034, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-02-03", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [3056, "ERR1396800", "ERX1468059", "ERS1051431", "ERP013615", "PRJEB12173", "Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts", "Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011", "Transcriptome Analysis", "Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.", "ArrayExpress:E ERAD 449", null, null, "zmp ph228 drosha A9", "SAMEA3864297", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864297|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:25Z|INSDC status:public|Submitter Id:29e942e0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29e942e0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "SC EXP 18732 1#7", "15616941", "Illumina sequencing of library 15616941 constructed from sample accession ERS1051431 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CAGATC.", "Small RNA miRNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP013615", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16", "18732_1#7.cram", "cram", 294666500.0, 5893330.0, "SC RUN 18732 1#7", "0:50", "A:85765921;C:76239559;G:76452231;T:56180868;N:27921", 50, null, null, null, 85765921, 76239559, 76452231, 56180868, 27921, "ERX1468059", "ERS1051431", "ERA612385", "European Nucleotide Archive", "Wellcome Sanger Institute", 1, 0.56455, null, 0.10217, null, 0.88286, null, 0.60374, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-02-03", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [3057, "ERR1396799", "ERX1468058", "ERS1051430", "ERP013615", "PRJEB12173", "Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts", "Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011", "Transcriptome Analysis", "Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.", "ArrayExpress:E ERAD 449", null, null, "zmp ph228 drosha A6", "SAMEA3864296", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864296|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:25Z|INSDC status:public|Submitter Id:29e06940 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29e06940 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "SC EXP 18732 1#6", "15616929", "Illumina sequencing of library 15616929 constructed from sample accession ERS1051430 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GCCAAT.", "Small RNA miRNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP013615", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16", "18732_1#6.cram", "cram", 239549350.0, 4790987.0, "SC RUN 18732 1#6", "0:50", "A:68726161;C:60828350;G:62739441;T:47232484;N:22914", 50, null, null, null, 68726161, 60828350, 62739441, 47232484, 22914, "ERX1468058", "ERS1051430", "ERA612385", "European Nucleotide Archive", "Wellcome Sanger Institute", 1, 0.64469, null, 0.1021, null, 0.88878, null, 0.58044, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-02-03", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [3058, "ERR1396798", "ERX1468057", "ERS1051429", "ERP013615", "PRJEB12173", "Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts", "Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011", "Transcriptome Analysis", "Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.", "ArrayExpress:E ERAD 449", null, null, "zmp ph228 drosha A1", "SAMEA3864295", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864295|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:24Z|INSDC status:public|Submitter Id:29d74180 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29d74180 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "SC EXP 18732 1#5", "15616917", "Illumina sequencing of library 15616917 constructed from sample accession ERS1051429 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ACAGTG.", "Small RNA miRNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP013615", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16", "18732_1#5.cram", "cram", 165341300.0, 3306826.0, "SC RUN 18732 1#5", "0:50", "A:47735538;C:41622088;G:43392205;T:32575765;N:15704", 50, null, null, null, 47735538, 41622088, 43392205, 32575765, 15704, "ERX1468057", "ERS1051429", "ERA612385", "European Nucleotide Archive", "Wellcome Sanger Institute", 1, 0.64704, null, 0.09836, null, 0.90534, null, 0.56172, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-02-03", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [3059, "ERR1396797", "ERX1468056", "ERS1051428", "ERP013615", "PRJEB12173", "Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts", "Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011", "Transcriptome Analysis", "Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.", "ArrayExpress:E ERAD 449", null, null, "zmp ph228 drosha B12", "SAMEA3864294", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864294|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:23Z|INSDC status:public|Submitter Id:29cf7950 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29cf7950 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "SC EXP 18732 1#4", "15616905", "Illumina sequencing of library 15616905 constructed from sample accession ERS1051428 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence TGACCA.", "Small RNA miRNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP013615", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16", "18732_1#4.cram", "cram", 401336200.0, 8026724.0, "SC RUN 18732 1#4", "0:50", "A:117609087;C:105872656;G:100576681;T:77238881;N:38895", 50, null, null, null, 117609087, 105872656, 100576681, 77238881, 38895, "ERX1468056", "ERS1051428", "ERA612385", "European Nucleotide Archive", "Wellcome Sanger Institute", 1, 0.51741, null, 0.10352, null, 0.89749, null, 0.58497, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-02-03", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [3060, "ERR1396796", "ERX1468055", "ERS1051427", "ERP013615", "PRJEB12173", "Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts", "Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011", "Transcriptome Analysis", "Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.", "ArrayExpress:E ERAD 449", null, null, "zmp ph228 drosha B10", "SAMEA3864293", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864293|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:22Z|INSDC status:public|Submitter Id:29c84d60 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29c84d60 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "SC EXP 18732 1#3", "15616893", "Illumina sequencing of library 15616893 constructed from sample accession ERS1051427 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence TTAGGC.", "Small RNA miRNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP013615", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16", "18732_1#3.cram", "cram", 214767600.0, 4295352.0, "SC RUN 18732 1#3", "0:50", "A:61527319;C:53911904;G:56445139;T:42862938;N:20300", 50, null, null, null, 61527319, 53911904, 56445139, 42862938, 20300, "ERX1468055", "ERS1051427", "ERA612385", "European Nucleotide Archive", "Wellcome Sanger Institute", 1, 0.57363, null, 0.11614, null, 0.88487, null, 0.61011, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-02-03", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [3061, "ERR1396795", "ERX1468054", "ERS1051426", "ERP013615", "PRJEB12173", "Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts", "Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011", "Transcriptome Analysis", "Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.", "ArrayExpress:E ERAD 449", null, null, "zmp ph228 drosha B7", "SAMEA3864292", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864292|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:22Z|INSDC status:public|Submitter Id:29b1df30 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29b1df30 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "SC EXP 18732 1#2", "15616881", "Illumina sequencing of library 15616881 constructed from sample accession ERS1051426 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CGATGT.", "Small RNA miRNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP013615", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16", "18732_1#2.cram", "cram", 326025150.0, 6520503.0, "SC RUN 18732 1#2", "0:50", "A:93261648;C:82767834;G:86798075;T:63166259;N:31334", 50, null, null, null, 93261648, 82767834, 86798075, 63166259, 31334, "ERX1468054", "ERS1051426", "ERA612385", "European Nucleotide Archive", "Wellcome Sanger Institute", 1, 0.57333, null, 0.11365, null, 0.87422, null, 0.60838, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-02-03", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [3062, "ERR1396794", "ERX1468053", "ERS1051425", "ERP013615", "PRJEB12173", "Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts", "Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011", "Transcriptome Analysis", "Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos.", "ArrayExpress:E ERAD 449", null, null, "zmp ph228 drosha B1", "SAMEA3864291", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864291|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:55Z|INSDC last update:2016 02 03T09:48:20Z|INSDC status:public|Submitter Id:29904d70 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29904d70 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing", "SC EXP 18732 1#1", "15616869", "Illumina sequencing of library 15616869 constructed from sample accession ERS1051425 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ATCACG.", "Small RNA miRNA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP013615", "Illumina HiSeq 2500 sequencing", "ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16", "18732_1#1.cram", "cram", 419669000.0, 8393380.0, "SC RUN 18732 1#1", "0:50", "A:121378853;C:106010609;G:109826454;T:82412717;N:40367", 50, null, null, null, 121378853, 106010609, 109826454, 82412717, 40367, "ERX1468053", "ERS1051425", "ERA612385", "European Nucleotide Archive", "Wellcome Sanger Institute", 1, 0.60815, null, 0.11567, null, 0.90289, null, 0.5657, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-02-03", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [5879, "ERR1759701", "ERX1826022", "ERS1474296", "ERP020578", "PRJEB18632", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E-MTAB-5323", "Transcriptome Analysis", "The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes.", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323", null, "Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Sample2", "SAMEA27136168", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute", "ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27136168|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample2|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:actn2 tdEodncv44Tg|sample name:E MTAB 5323:Sample2", null, null, null, null, null, null, null, null, "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E MTAB 5323:Sample2 s", "Sample2 s", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture\u2019s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "ERP020578", "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16", "mochizukis_lab_myl7_actn2tdEos_72h_01.fastq.gz", "fastq", 448234901.0, 6016977.0, "E MTAB 5323:Sample2", "0:74.50 1:0", "A:118923409;C:100586009;G:99987046;T:126071553;N:2666884", 74, 0, null, null, 118923409, 100586009, 99987046, 126071553, 2666884, "ERX1826022", "ERS1474296", "ERA776061", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", 1, 0.88465, null, 0.27583, null, 0.75398, null, 0.55917, null, 75, null, "B", null, "usable mapping rate", "illumina", "miseq", "full_length", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Japan", "2016-12-15", "Larval", "Larval", "Heart", "Cardiovascular System"], [5880, "ERR1759702", "ERX1826022", "ERS1474296", "ERP020578", "PRJEB18632", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E-MTAB-5323", "Transcriptome Analysis", "The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes.", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323", null, "Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Sample2", "SAMEA27136168", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute", "ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27136168|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample2|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:actn2 tdEodncv44Tg|sample name:E MTAB 5323:Sample2", null, null, null, null, null, null, null, null, "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E MTAB 5323:Sample2 s", "Sample2 s", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture\u2019s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "ERP020578", "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16", "mochizukis_lab_myl7_actn2tdEos_72h_02.fastq.gz", "fastq", 448116860.0, 6016977.0, "E MTAB 5323:Sample2 1", "0:0 1:74.48", "A:127811460;C:99875207;G:106561979;T:113792335;N:75879", 0, 74, null, null, 127811460, 99875207, 106561979, 113792335, 75879, "ERX1826022", "ERS1474296", "ERA776061", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", 1, 0.91589, null, 0.2509, null, 0.79005, null, 0.54852, null, 75, null, "B", null, "usable mapping rate", "illumina", "miseq", "full_length", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Japan", "2016-12-15", "Larval", "Larval", "Heart", "Cardiovascular System"], [5881, "ERR1759699", "ERX1826021", "ERS1474295", "ERP020578", "PRJEB18632", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E-MTAB-5323", "Transcriptome Analysis", "The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes.", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323", null, "Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Sample1", "SAMEA27135418", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute", "ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27135418|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample1|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:Nls mCherryncv11Tg|sample name:E MTAB 5323:Sample1", null, null, null, null, null, null, null, null, "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E MTAB 5323:Sample1 s", "Sample1 s", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture\u2019s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "ERP020578", "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16", "mochizukis_lab_myl7_NLSmCherry_72h_01.fastq.gz", "fastq", 766363334.0, 10284347.0, "E MTAB 5323:Sample1", "0:74.52 1:0", "A:201960096;C:174999154;G:173403690;T:211341998;N:4658396", 74, 0, null, null, 201960096, 174999154, 173403690, 211341998, 4658396, "ERX1826021", "ERS1474295", "ERA776061", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", 1, 0.86003, null, 0.20554, null, 0.76301, null, 0.55753, null, 74, null, "B", null, "usable mapping rate", "illumina", "miseq", "full_length", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Japan", "2016-12-15", "Larval", "Larval", "Heart", "Cardiovascular System"], [5882, "ERR1759700", "ERX1826021", "ERS1474295", "ERP020578", "PRJEB18632", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E-MTAB-5323", "Transcriptome Analysis", "The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes.", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323", null, "Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Sample1", "SAMEA27135418", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute", "ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27135418|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample1|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:Nls mCherryncv11Tg|sample name:E MTAB 5323:Sample1", null, null, null, null, null, null, null, null, "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E MTAB 5323:Sample1 s", "Sample1 s", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture\u2019s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "ERP020578", "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16", "mochizukis_lab_myl7_NLSmCHerry_72h_02.fastq.gz", "fastq", 766251339.0, 10284347.0, "E MTAB 5323:Sample1 1", "0:0 1:74.51", "A:214234414;C:174215653;G:180382062;T:197361982;N:57228", 0, 74, null, null, 214234414, 174215653, 180382062, 197361982, 57228, "ERX1826021", "ERS1474295", "ERA776061", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", 1, 0.87766, null, 0.21561, null, 0.77477, null, 0.53919, null, 73, null, "B", null, "usable mapping rate", "illumina", "miseq", "full_length", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Japan", "2016-12-15", "Larval", "Larval", "Heart", "Cardiovascular System"], [8104, "ERR2455366", "ERX2474426", "ERS2327331", "ERP107743", "PRJEB25789", "RNA seq of zebrafish larvae fed with different diets", "E-MTAB-6636", "Transcriptome Analysis", "We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development.", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29", null, "Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Sample 4", "SAMEA104725948", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College", "ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725948|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 4|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:overfeeding|organism part:liver|sample name:E MTAB 6636:Sample 4|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "E MTAB 6636:Sample 4 s", "Sample 4 s", "RNA seq of zebrafish larvae fed with different diets", "Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Experimental Factor: diet:overfeeding", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP107743", "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16", "OF-4_H7MWNALXX_L6_1.fq.gz", "fastq", 4961276550.0, 33075177.0, "E MTAB 6636:Sample 4", "0:150 1:0", "A:1349413168;C:1135314970;G:1137935563;T:1338034716;N:578133", 150, 0, null, null, 1349413168, 1135314970, 1137935563, 1338034716, 578133, "ERX2474426", "ERS2327331", "ERA1259907", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", 1, 0.90787, null, 0.11999, null, 0.66123, null, 0.49072, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2018-03-29", "Larval", "Larval", "Liver", "Liver and Biliary System"], [8105, "ERR2455365", "ERX2474425", "ERS2327330", "ERP107743", "PRJEB25789", "RNA seq of zebrafish larvae fed with different diets", "E-MTAB-6636", "Transcriptome Analysis", "We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development.", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29", null, "Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Sample 3", "SAMEA104725947", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College", "ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725947|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:fructose|organism part:liver|sample name:E MTAB 6636:Sample 3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "E MTAB 6636:Sample 3 s", "Sample 3 s", "RNA seq of zebrafish larvae fed with different diets", "Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Experimental Factor: diet:fructose", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP107743", "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16", "Fru-3_H7MWNALXX_L5_1.fq.gz", "fastq", 5858273250.0, 39055155.0, "E MTAB 6636:Sample 3", "0:150 1:0", "A:1580150663;C:1353221682;G:1355865524;T:1568428138;N:607243", 150, 0, null, null, 1580150663, 1353221682, 1355865524, 1568428138, 607243, "ERX2474425", "ERS2327330", "ERA1259907", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", 1, 0.91505, null, 0.11036, null, 0.65985, null, 0.48443, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2018-03-29", "Larval", "Larval", "Liver", "Liver and Biliary System"], [8106, "ERR2455364", "ERX2474424", "ERS2327329", "ERP107743", "PRJEB25789", "RNA seq of zebrafish larvae fed with different diets", "E-MTAB-6636", "Transcriptome Analysis", "We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development.", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29", null, "Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Sample 2", "SAMEA104725946", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College", "ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725946|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:cholesterol|organism part:liver|sample name:E MTAB 6636:Sample 2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "E MTAB 6636:Sample 2 s", "Sample 2 s", "RNA seq of zebrafish larvae fed with different diets", "Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Experimental Factor: diet:cholesterol", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP107743", "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16", "Cho-2_H7MWNALXX_L5_1.fq.gz", "fastq", 5636304900.0, 37575366.0, "E MTAB 6636:Sample 2", "0:150 1:0", "A:1526862069;C:1295343770;G:1298751994;T:1514766898;N:580169", 150, 0, null, null, 1526862069, 1295343770, 1298751994, 1514766898, 580169, "ERX2474424", "ERS2327329", "ERA1259907", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", 1, 0.91032, null, 0.11644, null, 0.66649, null, 0.47766, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2018-03-29", "Larval", "Larval", "Liver", "Liver and Biliary System"], [8107, "ERR2455363", "ERX2474423", "ERS2327328", "ERP107743", "PRJEB25789", "RNA seq of zebrafish larvae fed with different diets", "E-MTAB-6636", "Transcriptome Analysis", "We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development.", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29", null, "Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Sample 1", "SAMEA104725945", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College", "ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725945|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:control|organism part:liver|sample name:E MTAB 6636:Sample 1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "E MTAB 6636:Sample 1 s", "Sample 1 s", "RNA seq of zebrafish larvae fed with different diets", "Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Experimental Factor: diet:control", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP107743", "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16", "ND-1_H7MWNALXX_L5_1.fq.gz", "fastq", 5197165350.0, 34647769.0, "E MTAB 6636:Sample 1", "0:150 1:0", "A:1430911816;C:1174811274;G:1175616551;T:1415284019;N:541690", 150, 0, null, null, 1430911816, 1174811274, 1175616551, 1415284019, 541690, "ERX2474423", "ERS2327328", "ERA1259907", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", 1, 0.89838, null, 0.13883, null, 0.66129, null, 0.48467, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2018-03-29", "Larval", "Larval", "Liver", "Liver and Biliary System"], [9361, "ERR3011947", "ERX3014407", "ERS2994081", "ERP112907", "PRJEB30451", "Effects of anti androgenic compounds on zebrafish insulin mutants", "E-MTAB-7283", "Transcriptome Analysis", "Aiming to identify insulin independent modulators of glucose homeostasis we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists. To investigate how AR antagonism mediates glucose level reduction in ins mutants we evaluated the effects of antagonist treatment using transcriptomic studies. RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.", "ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18", null, "Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "Flutamide 2", "SAMEA5186582", "Max Planck Institute for Heart and Lung Research", "ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186582|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Flutamide 2|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Flutamide 2|scientific name:Danio rerio|strain:ins bns102", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "E MTAB 7283:Flutamide 2 s", "Flutamide 2 s", "Effects of anti androgenic compounds on zebrafish insulin mutants", "insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "Experimental Factor: compound:flutamide|Experimental Factor: dose:10", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP112907", "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18", "Teja_Flutamide_2_R1.fastq.gz", "fastq", 1754963940.0, 23552243.0, "E MTAB 7283:Flutamide 2", "0:74.51 1:0", "A:455444321;C:410713896;G:385640226;T:503155736;N:9761", 74, 0, null, null, 455444321, 410713896, 385640226, 503155736, 9761, "ERX3014407", "ERS2994081", "ERA1697296", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.94351, null, 0.11595, null, 0.67483, null, 0.48762, null, 73, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-12-18", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9362, "ERR3011946", "ERX3014406", "ERS2994080", "ERP112907", "PRJEB30451", "Effects of anti androgenic compounds on zebrafish insulin mutants", "E-MTAB-7283", "Transcriptome Analysis", "Aiming to identify insulin independent modulators of glucose homeostasis we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists. To investigate how AR antagonism mediates glucose level reduction in ins mutants we evaluated the effects of antagonist treatment using transcriptomic studies. RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.", "ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18", null, "Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "Flutamide 1", "SAMEA5186581", "Max Planck Institute for Heart and Lung Research", "ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186581|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Flutamide 1|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Flutamide 1|scientific name:Danio rerio|strain:ins bns102", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "E MTAB 7283:Flutamide 1 s", "Flutamide 1 s", "Effects of anti androgenic compounds on zebrafish insulin mutants", "insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "Experimental Factor: compound:flutamide|Experimental Factor: dose:10", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP112907", "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18", "Teja_Flutamide_1_R1.fastq.gz", "fastq", 1631102863.0, 21898245.0, "E MTAB 7283:Flutamide 1", "0:74.49 1:0", "A:424378341;C:380806325;G:358128992;T:467779945;N:9260", 74, 0, null, null, 424378341, 380806325, 358128992, 467779945, 9260, "ERX3014406", "ERS2994080", "ERA1697296", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.94332, null, 0.11797, null, 0.67596, null, 0.48847, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-12-18", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9363, "ERR3011945", "ERX3014405", "ERS2994079", "ERP112907", "PRJEB30451", "Effects of anti androgenic compounds on zebrafish insulin mutants", "E-MTAB-7283", "Transcriptome Analysis", "Aiming to identify insulin independent modulators of glucose homeostasis we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists. To investigate how AR antagonism mediates glucose level reduction in ins mutants we evaluated the effects of antagonist treatment using transcriptomic studies. RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.", "ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18", null, "Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "DMSO 2", "SAMEA5186580", "Max Planck Institute for Heart and Lung Research", "ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186580|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:DMSO 2|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:DMSO 2|scientific name:Danio rerio|strain:ins bns102", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "E MTAB 7283:DMSO 2 s", "DMSO 2 s", "Effects of anti androgenic compounds on zebrafish insulin mutants", "insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "Experimental Factor: compound:dimethyl sulfoxide|Experimental Factor: dose:1", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP112907", "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18", "Teja_DMSO_2_R1.fastq.gz", "fastq", 1811573293.0, 24316929.0, "E MTAB 7283:DMSO 2", "0:74.50 1:0", "A:470888315;C:423635861;G:396796840;T:520242179;N:10098", 74, 0, null, null, 470888315, 423635861, 396796840, 520242179, 10098, "ERX3014405", "ERS2994079", "ERA1697296", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.94219, null, 0.12305, null, 0.67184, null, 0.47704, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-12-18", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9364, "ERR3011944", "ERX3014404", "ERS2994078", "ERP112907", "PRJEB30451", "Effects of anti androgenic compounds on zebrafish insulin mutants", "E-MTAB-7283", "Transcriptome Analysis", "Aiming to identify insulin independent modulators of glucose homeostasis we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists. To investigate how AR antagonism mediates glucose level reduction in ins mutants we evaluated the effects of antagonist treatment using transcriptomic studies. RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.", "ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18", null, "Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "DMSO 1", "SAMEA5186579", "Max Planck Institute for Heart and Lung Research", "ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186579|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:DMSO 1|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:DMSO 1|scientific name:Danio rerio|strain:ins bns102", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "E MTAB 7283:DMSO 1 s", "DMSO 1 s", "Effects of anti androgenic compounds on zebrafish insulin mutants", "insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "Experimental Factor: compound:dimethyl sulfoxide|Experimental Factor: dose:1", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP112907", "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18", "Teja_DMSO_1_R1.fastq.gz", "fastq", 1609807409.0, 21611475.0, "E MTAB 7283:DMSO 1", "0:74.49 1:0", "A:420253680;C:374436301;G:352526427;T:462581933;N:9068", 74, 0, null, null, 420253680, 374436301, 352526427, 462581933, 9068, "ERX3014404", "ERS2994078", "ERA1697296", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.94094, null, 0.12292, null, 0.67006, null, 0.48442, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-12-18", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9365, "ERR3011943", "ERX3014403", "ERS2994077", "ERP112907", "PRJEB30451", "Effects of anti androgenic compounds on zebrafish insulin mutants", "E-MTAB-7283", "Transcriptome Analysis", "Aiming to identify insulin independent modulators of glucose homeostasis we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists. To investigate how AR antagonism mediates glucose level reduction in ins mutants we evaluated the effects of antagonist treatment using transcriptomic studies. RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.", "ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18", null, "Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "Cyproter1 2", "SAMEA5186578", "Max Planck Institute for Heart and Lung Research", "ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186578|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Cyproter1 2|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Cyproter1 2|scientific name:Danio rerio|strain:ins bns102", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "E MTAB 7283:Cyproterone 2 s", "Cyproterone 2 s", "Effects of anti androgenic compounds on zebrafish insulin mutants", "insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "Experimental Factor: compound:cyproter1|Experimental Factor: dose:10", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP112907", "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18", "Teja_Cyproterone_2_R1.fastq.gz", "fastq", 1823142918.0, 24468337.0, "E MTAB 7283:Cyproterone 2", "0:74.51 1:0", "A:469387174;C:428783310;G:403791044;T:521171021;N:10369", 74, 0, null, null, 469387174, 428783310, 403791044, 521171021, 10369, "ERX3014403", "ERS2994077", "ERA1697296", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.9432, null, 0.11718, null, 0.67389, null, 0.4768, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-12-18", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9366, "ERR3011942", "ERX3014402", "ERS2994076", "ERP112907", "PRJEB30451", "Effects of anti androgenic compounds on zebrafish insulin mutants", "E-MTAB-7283", "Transcriptome Analysis", "Aiming to identify insulin independent modulators of glucose homeostasis we performed a drug screen on zebrafish insulin ins mutants and identified androgen receptor AR antagonists. To investigate how AR antagonism mediates glucose level reduction in ins mutants we evaluated the effects of antagonist treatment using transcriptomic studies. RNA Seq analyses were performed on 120 hpf ins mutants treated with Flutamide or Cyproterone starting at 84 hpf compared to vehicle DMSO treated mutants.", "ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18", null, "Protocols: insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "Cyproter1 1", "SAMEA5186577", "Max Planck Institute for Heart and Lung Research", "ENA FIRST PUBLIC:2018 12 21T17:03:09Z|ENA LAST UPDATE:2018 12 18T09:28:56Z|External Id:SAMEA5186577|INSDC center name:Max Planck Institute for Heart and Lung Research|INSDC first public:2018 12 21T17:03:09Z|INSDC last update:2018 12 18T09:28:56Z|INSDC status:public|Submitter Id:E MTAB 7283:Cyproter1 1|age:120|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:ins CRISPR/Cas9 mediated knockout|individual:mixed pool of 10 embryos|organism part:whole organism|sample name:E MTAB 7283:Cyproter1 1|scientific name:Danio rerio|strain:ins bns102", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "E MTAB 7283:Cyproterone 1 s", "Cyproterone 1 s", "Effects of anti androgenic compounds on zebrafish insulin mutants", "insulin mutant embryos were obtained from two different crosses biological replicates. Embryos were grown at 28 degrees C in egg water. 10 animals per sample were pooled water was removed and Trizol was added. Animals were treated with 1% DMSO or Flutamide 10 micromolar or Cyproterone 10 micromolar from 84 hpf to 120 hpf. Total RNA was isolated from 120 hpf zebrafish using the RNA Clean & Concentrator kit Zymo Research combined with DNase digestion RNase free DNase Set Promega to avoid contamination by genomic DNA. 3\u00b5g of total RNA was used as input for Truseq Stranded mRNA Library preparation following manufacture's low sample protocol Illumina", "Experimental Factor: compound:cyproter1|Experimental Factor: dose:10", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP112907", "NextSeq 500 sequencing; Effects of anti androgenic compounds on zebrafish insulin mutants", "ENA FIRST PUBLIC:2018 12 21|ENA LAST UPDATE:2018 12 18", "Teja_Cyproterone_1_R1.fastq.gz", "fastq", 1901027130.0, 25512731.0, "E MTAB 7283:Cyproterone 1", "0:74.51 1:0", "A:487302419;C:449208827;G:422183780;T:542321577;N:10527", 74, 0, null, null, 487302419, 449208827, 422183780, 542321577, 10527, "ERX3014402", "ERS2994076", "ERA1697296", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.94427, null, 0.11318, null, 0.67294, null, 0.47183, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-12-18", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9651, "ERR3266392", "ERX3293003", "ERS3358386", "ERP114712", "PRJEB32081", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E-MTAB-7846", "Transcriptome Analysis", "To investigate the activity of sponge enhancers in vertebrates transgenic experiments was performed where sponge enhancers were inserted into zebrafish embryos and stable lines generated abstract: Transcription factors TFs bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs the evolution of enhancers has been difficult to trace because of their fast evolution. Here we take enhancers in the sponge Amphimedon queenslandica and test their activity in zebrafish and mouse. Of the five sponge enhancers assessed three were located in conserved syntenic gene regions that are unique to animals Islet\u2013Scaper Ccne1\u2013Uri Tdrd3\u2013Diaph3. Despite diverging over 700 million yrs ago and a dearth of sequence identity sponge enhancers are able to drive cell type specific reporter gene expression in vertebrates. Analysis of the type and frequency of TF binding motifs in the sponge Islet enhancer allowed for the identification of homologous enhancers in human and mouse which show remarkably similar reporter expression patterns to the sponge enhancer. These findings uncover an unexpected deep conservation of enhancers and suggest that enhancers established early in metazoan evolution can remain functional through retention of combinations of transcription factor binding motifs despite substantial sequence divergence.", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", null, "Protocols: 72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "sponge tdr gfp positive rep2", "SAMEA5556346", "UQ", "ENA FIRST PUBLIC:2019 11 30T04:02:56Z|ENA LAST UPDATE:2019 04 08T12:20:25Z|External Id:SAMEA5556346|INSDC center name:UQ|INSDC first public:2019 11 30T04:02:56Z|INSDC last update:2019 04 08T12:20:25Z|INSDC status:public|Submitter Id:E MTAB 7846:sponge tdr gfp positive rep2|age:72|broker name:ArrayExpress|cell type:GFP positive|common name:zebrafish|developmental stage:larval protruding mouth|genotype:Tgstdrd3 diaph3:eGFPuq7mf|individual:pool 6|organism part:zebrafish comp1nt|sample name:E MTAB 7846:sponge tdr gfp positive rep2|scientific name:Danio rerio|sex:both|strain:A/B or Tu strains", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E MTAB 7846:sponge tdr gfp positive rep2 s", "sponge tdr gfp positive rep2 s", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "Experimental Factor: genotype:Tgstdrd3 diaph3:eGFPuq7mf|Experimental Factor: cell type:GFP positive", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP114712", "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", "E9_9pos_S2_L001_R1_001.fastq.gz", "fastq", 603238067.0, 8014716.0, "E MTAB 7846:sponge tdr gfp positive rep2 lane1", "0:75.27 1:0", "A:164797697;C:136552121;G:141138007;T:160737152;N:13090", 75, 0, null, null, 164797697, 136552121, 141138007, 160737152, 13090, "ERX3293003", "ERS3358386", "ERA1822647", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.95083, null, 0.06432, null, 0.71532, null, 0.50098, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Unknown", "2019-04-08", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9652, "ERR3266393", "ERX3293003", "ERS3358386", "ERP114712", "PRJEB32081", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E-MTAB-7846", "Transcriptome Analysis", "To investigate the activity of sponge enhancers in vertebrates transgenic experiments was performed where sponge enhancers were inserted into zebrafish embryos and stable lines generated abstract: Transcription factors TFs bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs the evolution of enhancers has been difficult to trace because of their fast evolution. Here we take enhancers in the sponge Amphimedon queenslandica and test their activity in zebrafish and mouse. Of the five sponge enhancers assessed three were located in conserved syntenic gene regions that are unique to animals Islet\u2013Scaper Ccne1\u2013Uri Tdrd3\u2013Diaph3. Despite diverging over 700 million yrs ago and a dearth of sequence identity sponge enhancers are able to drive cell type specific reporter gene expression in vertebrates. Analysis of the type and frequency of TF binding motifs in the sponge Islet enhancer allowed for the identification of homologous enhancers in human and mouse which show remarkably similar reporter expression patterns to the sponge enhancer. These findings uncover an unexpected deep conservation of enhancers and suggest that enhancers established early in metazoan evolution can remain functional through retention of combinations of transcription factor binding motifs despite substantial sequence divergence.", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", null, "Protocols: 72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "sponge tdr gfp positive rep2", "SAMEA5556346", "UQ", "ENA FIRST PUBLIC:2019 11 30T04:02:56Z|ENA LAST UPDATE:2019 04 08T12:20:25Z|External Id:SAMEA5556346|INSDC center name:UQ|INSDC first public:2019 11 30T04:02:56Z|INSDC last update:2019 04 08T12:20:25Z|INSDC status:public|Submitter Id:E MTAB 7846:sponge tdr gfp positive rep2|age:72|broker name:ArrayExpress|cell type:GFP positive|common name:zebrafish|developmental stage:larval protruding mouth|genotype:Tgstdrd3 diaph3:eGFPuq7mf|individual:pool 6|organism part:zebrafish comp1nt|sample name:E MTAB 7846:sponge tdr gfp positive rep2|scientific name:Danio rerio|sex:both|strain:A/B or Tu strains", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E MTAB 7846:sponge tdr gfp positive rep2 s", "sponge tdr gfp positive rep2 s", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "Experimental Factor: genotype:Tgstdrd3 diaph3:eGFPuq7mf|Experimental Factor: cell type:GFP positive", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP114712", "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", "E9_9pos_S2_L002_R1_001.fastq.gz", "fastq", 603749720.0, 8021069.0, "E MTAB 7846:sponge tdr gfp positive rep2 lane2", "0:75.27 1:0", "A:164972969;C:136661417;G:141205792;T:160896264;N:13278", 75, 0, null, null, 164972969, 136661417, 141205792, 160896264, 13278, "ERX3293003", "ERS3358386", "ERA1822647", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.951, null, 0.06542, null, 0.71768, null, 0.50051, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Unknown", "2019-04-08", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9653, "ERR3266394", "ERX3293003", "ERS3358386", "ERP114712", "PRJEB32081", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E-MTAB-7846", "Transcriptome Analysis", "To investigate the activity of sponge enhancers in vertebrates transgenic experiments was performed where sponge enhancers were inserted into zebrafish embryos and stable lines generated abstract: Transcription factors TFs bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs the evolution of enhancers has been difficult to trace because of their fast evolution. Here we take enhancers in the sponge Amphimedon queenslandica and test their activity in zebrafish and mouse. Of the five sponge enhancers assessed three were located in conserved syntenic gene regions that are unique to animals Islet\u2013Scaper Ccne1\u2013Uri Tdrd3\u2013Diaph3. Despite diverging over 700 million yrs ago and a dearth of sequence identity sponge enhancers are able to drive cell type specific reporter gene expression in vertebrates. Analysis of the type and frequency of TF binding motifs in the sponge Islet enhancer allowed for the identification of homologous enhancers in human and mouse which show remarkably similar reporter expression patterns to the sponge enhancer. These findings uncover an unexpected deep conservation of enhancers and suggest that enhancers established early in metazoan evolution can remain functional through retention of combinations of transcription factor binding motifs despite substantial sequence divergence.", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", null, "Protocols: 72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "sponge tdr gfp positive rep2", "SAMEA5556346", "UQ", "ENA FIRST PUBLIC:2019 11 30T04:02:56Z|ENA LAST UPDATE:2019 04 08T12:20:25Z|External Id:SAMEA5556346|INSDC center name:UQ|INSDC first public:2019 11 30T04:02:56Z|INSDC last update:2019 04 08T12:20:25Z|INSDC status:public|Submitter Id:E MTAB 7846:sponge tdr gfp positive rep2|age:72|broker name:ArrayExpress|cell type:GFP positive|common name:zebrafish|developmental stage:larval protruding mouth|genotype:Tgstdrd3 diaph3:eGFPuq7mf|individual:pool 6|organism part:zebrafish comp1nt|sample name:E MTAB 7846:sponge tdr gfp positive rep2|scientific name:Danio rerio|sex:both|strain:A/B or Tu strains", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E MTAB 7846:sponge tdr gfp positive rep2 s", "sponge tdr gfp positive rep2 s", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "Experimental Factor: genotype:Tgstdrd3 diaph3:eGFPuq7mf|Experimental Factor: cell type:GFP positive", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP114712", "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", "E9_9pos_S2_L003_R1_001.fastq.gz", "fastq", 608154053.0, 8079704.0, "E MTAB 7846:sponge tdr gfp positive rep2 lane3", "0:75.27 1:0", "A:166117918;C:137731172;G:142320339;T:161970092;N:14532", 75, 0, null, null, 166117918, 137731172, 142320339, 161970092, 14532, "ERX3293003", "ERS3358386", "ERA1822647", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.95155, null, 0.0657, null, 0.71634, null, 0.49493, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Unknown", "2019-04-08", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9654, "ERR3266395", "ERX3293003", "ERS3358386", "ERP114712", "PRJEB32081", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E-MTAB-7846", "Transcriptome Analysis", "To investigate the activity of sponge enhancers in vertebrates transgenic experiments was performed where sponge enhancers were inserted into zebrafish embryos and stable lines generated abstract: Transcription factors TFs bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs the evolution of enhancers has been difficult to trace because of their fast evolution. Here we take enhancers in the sponge Amphimedon queenslandica and test their activity in zebrafish and mouse. Of the five sponge enhancers assessed three were located in conserved syntenic gene regions that are unique to animals Islet\u2013Scaper Ccne1\u2013Uri Tdrd3\u2013Diaph3. Despite diverging over 700 million yrs ago and a dearth of sequence identity sponge enhancers are able to drive cell type specific reporter gene expression in vertebrates. Analysis of the type and frequency of TF binding motifs in the sponge Islet enhancer allowed for the identification of homologous enhancers in human and mouse which show remarkably similar reporter expression patterns to the sponge enhancer. These findings uncover an unexpected deep conservation of enhancers and suggest that enhancers established early in metazoan evolution can remain functional through retention of combinations of transcription factor binding motifs despite substantial sequence divergence.", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", null, "Protocols: 72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "sponge tdr gfp positive rep2", "SAMEA5556346", "UQ", "ENA FIRST PUBLIC:2019 11 30T04:02:56Z|ENA LAST UPDATE:2019 04 08T12:20:25Z|External Id:SAMEA5556346|INSDC center name:UQ|INSDC first public:2019 11 30T04:02:56Z|INSDC last update:2019 04 08T12:20:25Z|INSDC status:public|Submitter Id:E MTAB 7846:sponge tdr gfp positive rep2|age:72|broker name:ArrayExpress|cell type:GFP positive|common name:zebrafish|developmental stage:larval protruding mouth|genotype:Tgstdrd3 diaph3:eGFPuq7mf|individual:pool 6|organism part:zebrafish comp1nt|sample name:E MTAB 7846:sponge tdr gfp positive rep2|scientific name:Danio rerio|sex:both|strain:A/B or Tu strains", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E MTAB 7846:sponge tdr gfp positive rep2 s", "sponge tdr gfp positive rep2 s", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "Experimental Factor: genotype:Tgstdrd3 diaph3:eGFPuq7mf|Experimental Factor: cell type:GFP positive", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP114712", "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", "E9_9pos_S2_L004_R1_001.fastq.gz", "fastq", 599143392.0, 7959897.0, "E MTAB 7846:sponge tdr gfp positive rep2 lane4", "0:75.27 1:0", "A:163706904;C:135622453;G:140192351;T:159605249;N:16435", 75, 0, null, null, 163706904, 135622453, 140192351, 159605249, 16435, "ERX3293003", "ERS3358386", "ERA1822647", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.95061, null, 0.06431, null, 0.71764, null, 0.50166, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Unknown", "2019-04-08", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9655, "ERR3266388", "ERX3293002", "ERS3358385", "ERP114712", "PRJEB32081", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E-MTAB-7846", "Transcriptome Analysis", "To investigate the activity of sponge enhancers in vertebrates transgenic experiments was performed where sponge enhancers were inserted into zebrafish embryos and stable lines generated abstract: Transcription factors TFs bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs the evolution of enhancers has been difficult to trace because of their fast evolution. Here we take enhancers in the sponge Amphimedon queenslandica and test their activity in zebrafish and mouse. Of the five sponge enhancers assessed three were located in conserved syntenic gene regions that are unique to animals Islet\u2013Scaper Ccne1\u2013Uri Tdrd3\u2013Diaph3. Despite diverging over 700 million yrs ago and a dearth of sequence identity sponge enhancers are able to drive cell type specific reporter gene expression in vertebrates. Analysis of the type and frequency of TF binding motifs in the sponge Islet enhancer allowed for the identification of homologous enhancers in human and mouse which show remarkably similar reporter expression patterns to the sponge enhancer. These findings uncover an unexpected deep conservation of enhancers and suggest that enhancers established early in metazoan evolution can remain functional through retention of combinations of transcription factor binding motifs despite substantial sequence divergence.", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", null, "Protocols: 72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "sponge tdr gfp positive rep1", "SAMEA5556345", "UQ", "ENA FIRST PUBLIC:2019 11 30T04:02:56Z|ENA LAST UPDATE:2019 04 08T12:20:25Z|External Id:SAMEA5556345|INSDC center name:UQ|INSDC first public:2019 11 30T04:02:56Z|INSDC last update:2019 04 08T12:20:25Z|INSDC status:public|Submitter Id:E MTAB 7846:sponge tdr gfp positive rep1|age:72|broker name:ArrayExpress|cell type:GFP positive|common name:zebrafish|developmental stage:larval protruding mouth|genotype:Tgstdrd3 diaph3:eGFPuq7mf|individual:pool 5|organism part:zebrafish comp1nt|sample name:E MTAB 7846:sponge tdr gfp positive rep1|scientific name:Danio rerio|sex:both|strain:A/B or Tu strains", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E MTAB 7846:sponge tdr gfp positive rep1 s", "sponge tdr gfp positive rep1 s", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "Experimental Factor: genotype:Tgstdrd3 diaph3:eGFPuq7mf|Experimental Factor: cell type:GFP positive", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP114712", "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", "E9_6pos_S4_L001_R1_001.fastq.gz", "fastq", 616761505.0, 8202480.0, "E MTAB 7846:sponge tdr gfp positive rep1 lane1", "0:75.19 1:0", "A:168679238;C:139548565;G:143969797;T:164545362;N:18543", 75, 0, null, null, 168679238, 139548565, 143969797, 164545362, 18543, "ERX3293002", "ERS3358385", "ERA1822647", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.95019, null, 0.06806, null, 0.7097, null, 0.50337, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Unknown", "2019-04-08", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9656, "ERR3266389", "ERX3293002", "ERS3358385", "ERP114712", "PRJEB32081", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E-MTAB-7846", "Transcriptome Analysis", "To investigate the activity of sponge enhancers in vertebrates transgenic experiments was performed where sponge enhancers were inserted into zebrafish embryos and stable lines generated abstract: Transcription factors TFs bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs the evolution of enhancers has been difficult to trace because of their fast evolution. Here we take enhancers in the sponge Amphimedon queenslandica and test their activity in zebrafish and mouse. Of the five sponge enhancers assessed three were located in conserved syntenic gene regions that are unique to animals Islet\u2013Scaper Ccne1\u2013Uri Tdrd3\u2013Diaph3. Despite diverging over 700 million yrs ago and a dearth of sequence identity sponge enhancers are able to drive cell type specific reporter gene expression in vertebrates. Analysis of the type and frequency of TF binding motifs in the sponge Islet enhancer allowed for the identification of homologous enhancers in human and mouse which show remarkably similar reporter expression patterns to the sponge enhancer. These findings uncover an unexpected deep conservation of enhancers and suggest that enhancers established early in metazoan evolution can remain functional through retention of combinations of transcription factor binding motifs despite substantial sequence divergence.", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", null, "Protocols: 72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "sponge tdr gfp positive rep1", "SAMEA5556345", "UQ", "ENA FIRST PUBLIC:2019 11 30T04:02:56Z|ENA LAST UPDATE:2019 04 08T12:20:25Z|External Id:SAMEA5556345|INSDC center name:UQ|INSDC first public:2019 11 30T04:02:56Z|INSDC last update:2019 04 08T12:20:25Z|INSDC status:public|Submitter Id:E MTAB 7846:sponge tdr gfp positive rep1|age:72|broker name:ArrayExpress|cell type:GFP positive|common name:zebrafish|developmental stage:larval protruding mouth|genotype:Tgstdrd3 diaph3:eGFPuq7mf|individual:pool 5|organism part:zebrafish comp1nt|sample name:E MTAB 7846:sponge tdr gfp positive rep1|scientific name:Danio rerio|sex:both|strain:A/B or Tu strains", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E MTAB 7846:sponge tdr gfp positive rep1 s", "sponge tdr gfp positive rep1 s", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "Experimental Factor: genotype:Tgstdrd3 diaph3:eGFPuq7mf|Experimental Factor: cell type:GFP positive", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP114712", "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", "E9_6pos_S4_L002_R1_001.fastq.gz", "fastq", 617529482.0, 8212485.0, "E MTAB 7846:sponge tdr gfp positive rep1 lane2", "0:75.19 1:0", "A:168925757;C:139655387;G:144096837;T:164831236;N:20265", 75, 0, null, null, 168925757, 139655387, 144096837, 164831236, 20265, "ERX3293002", "ERS3358385", "ERA1822647", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.9492, null, 0.06753, null, 0.712, null, 0.49881, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Unknown", "2019-04-08", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9657, "ERR3266390", "ERX3293002", "ERS3358385", "ERP114712", "PRJEB32081", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E-MTAB-7846", "Transcriptome Analysis", "To investigate the activity of sponge enhancers in vertebrates transgenic experiments was performed where sponge enhancers were inserted into zebrafish embryos and stable lines generated abstract: Transcription factors TFs bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs the evolution of enhancers has been difficult to trace because of their fast evolution. Here we take enhancers in the sponge Amphimedon queenslandica and test their activity in zebrafish and mouse. Of the five sponge enhancers assessed three were located in conserved syntenic gene regions that are unique to animals Islet\u2013Scaper Ccne1\u2013Uri Tdrd3\u2013Diaph3. Despite diverging over 700 million yrs ago and a dearth of sequence identity sponge enhancers are able to drive cell type specific reporter gene expression in vertebrates. Analysis of the type and frequency of TF binding motifs in the sponge Islet enhancer allowed for the identification of homologous enhancers in human and mouse which show remarkably similar reporter expression patterns to the sponge enhancer. These findings uncover an unexpected deep conservation of enhancers and suggest that enhancers established early in metazoan evolution can remain functional through retention of combinations of transcription factor binding motifs despite substantial sequence divergence.", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", null, "Protocols: 72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "sponge tdr gfp positive rep1", "SAMEA5556345", "UQ", "ENA FIRST PUBLIC:2019 11 30T04:02:56Z|ENA LAST UPDATE:2019 04 08T12:20:25Z|External Id:SAMEA5556345|INSDC center name:UQ|INSDC first public:2019 11 30T04:02:56Z|INSDC last update:2019 04 08T12:20:25Z|INSDC status:public|Submitter Id:E MTAB 7846:sponge tdr gfp positive rep1|age:72|broker name:ArrayExpress|cell type:GFP positive|common name:zebrafish|developmental stage:larval protruding mouth|genotype:Tgstdrd3 diaph3:eGFPuq7mf|individual:pool 5|organism part:zebrafish comp1nt|sample name:E MTAB 7846:sponge tdr gfp positive rep1|scientific name:Danio rerio|sex:both|strain:A/B or Tu strains", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E MTAB 7846:sponge tdr gfp positive rep1 s", "sponge tdr gfp positive rep1 s", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "Experimental Factor: genotype:Tgstdrd3 diaph3:eGFPuq7mf|Experimental Factor: cell type:GFP positive", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP114712", "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", "E9_6pos_S4_L003_R1_001.fastq.gz", "fastq", 624156883.0, 8300861.0, "E MTAB 7846:sponge tdr gfp positive rep1 lane3", "0:75.19 1:0", "A:170696950;C:141302376;G:145759286;T:166377781;N:20490", 75, 0, null, null, 170696950, 141302376, 145759286, 166377781, 20490, "ERX3293002", "ERS3358385", "ERA1822647", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.94917, null, 0.06724, null, 0.71291, null, 0.50783, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Unknown", "2019-04-08", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9658, "ERR3266391", "ERX3293002", "ERS3358385", "ERP114712", "PRJEB32081", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E-MTAB-7846", "Transcriptome Analysis", "To investigate the activity of sponge enhancers in vertebrates transgenic experiments was performed where sponge enhancers were inserted into zebrafish embryos and stable lines generated abstract: Transcription factors TFs bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs the evolution of enhancers has been difficult to trace because of their fast evolution. Here we take enhancers in the sponge Amphimedon queenslandica and test their activity in zebrafish and mouse. Of the five sponge enhancers assessed three were located in conserved syntenic gene regions that are unique to animals Islet\u2013Scaper Ccne1\u2013Uri Tdrd3\u2013Diaph3. Despite diverging over 700 million yrs ago and a dearth of sequence identity sponge enhancers are able to drive cell type specific reporter gene expression in vertebrates. Analysis of the type and frequency of TF binding motifs in the sponge Islet enhancer allowed for the identification of homologous enhancers in human and mouse which show remarkably similar reporter expression patterns to the sponge enhancer. These findings uncover an unexpected deep conservation of enhancers and suggest that enhancers established early in metazoan evolution can remain functional through retention of combinations of transcription factor binding motifs despite substantial sequence divergence.", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", null, "Protocols: 72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "sponge tdr gfp positive rep1", "SAMEA5556345", "UQ", "ENA FIRST PUBLIC:2019 11 30T04:02:56Z|ENA LAST UPDATE:2019 04 08T12:20:25Z|External Id:SAMEA5556345|INSDC center name:UQ|INSDC first public:2019 11 30T04:02:56Z|INSDC last update:2019 04 08T12:20:25Z|INSDC status:public|Submitter Id:E MTAB 7846:sponge tdr gfp positive rep1|age:72|broker name:ArrayExpress|cell type:GFP positive|common name:zebrafish|developmental stage:larval protruding mouth|genotype:Tgstdrd3 diaph3:eGFPuq7mf|individual:pool 5|organism part:zebrafish comp1nt|sample name:E MTAB 7846:sponge tdr gfp positive rep1|scientific name:Danio rerio|sex:both|strain:A/B or Tu strains", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E MTAB 7846:sponge tdr gfp positive rep1 s", "sponge tdr gfp positive rep1 s", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "Experimental Factor: genotype:Tgstdrd3 diaph3:eGFPuq7mf|Experimental Factor: cell type:GFP positive", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP114712", "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", "E9_6pos_S4_L004_R1_001.fastq.gz", "fastq", 615013615.0, 8179180.0, "E MTAB 7846:sponge tdr gfp positive rep1 lane4", "0:75.19 1:0", "A:168237742;C:139106952;G:143535658;T:164110735;N:22528", 75, 0, null, null, 168237742, 139106952, 143535658, 164110735, 22528, "ERX3293002", "ERS3358385", "ERA1822647", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.94892, null, 0.06723, null, 0.71206, null, 0.50775, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Unknown", "2019-04-08", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9659, "ERR3266384", "ERX3293001", "ERS3358384", "ERP114712", "PRJEB32081", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E-MTAB-7846", "Transcriptome Analysis", "To investigate the activity of sponge enhancers in vertebrates transgenic experiments was performed where sponge enhancers were inserted into zebrafish embryos and stable lines generated abstract: Transcription factors TFs bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs the evolution of enhancers has been difficult to trace because of their fast evolution. Here we take enhancers in the sponge Amphimedon queenslandica and test their activity in zebrafish and mouse. Of the five sponge enhancers assessed three were located in conserved syntenic gene regions that are unique to animals Islet\u2013Scaper Ccne1\u2013Uri Tdrd3\u2013Diaph3. Despite diverging over 700 million yrs ago and a dearth of sequence identity sponge enhancers are able to drive cell type specific reporter gene expression in vertebrates. Analysis of the type and frequency of TF binding motifs in the sponge Islet enhancer allowed for the identification of homologous enhancers in human and mouse which show remarkably similar reporter expression patterns to the sponge enhancer. These findings uncover an unexpected deep conservation of enhancers and suggest that enhancers established early in metazoan evolution can remain functional through retention of combinations of transcription factor binding motifs despite substantial sequence divergence.", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", null, "Protocols: 72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "sponge tdr gfp negative rep2", "SAMEA5556344", "UQ", "ENA FIRST PUBLIC:2019 11 30T04:02:56Z|ENA LAST UPDATE:2019 04 08T12:20:25Z|External Id:SAMEA5556344|INSDC center name:UQ|INSDC first public:2019 11 30T04:02:56Z|INSDC last update:2019 04 08T12:20:25Z|INSDC status:public|Submitter Id:E MTAB 7846:sponge tdr gfp negative rep2|age:72|broker name:ArrayExpress|cell type:GFP negative|common name:zebrafish|developmental stage:larval protruding mouth|genotype:Tgstdrd3 diaph3:eGFPuq7mf|individual:pool 6|organism part:zebrafish comp1nt|sample name:E MTAB 7846:sponge tdr gfp negative rep2|scientific name:Danio rerio|sex:both|strain:A/B or Tu strains", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E MTAB 7846:sponge tdr gfp negative rep2 s", "sponge tdr gfp negative rep2 s", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "Experimental Factor: genotype:Tgstdrd3 diaph3:eGFPuq7mf|Experimental Factor: cell type:GFP negative", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP114712", "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", "E9_9neg_S1_L001_R1_001.fastq.gz", "fastq", 659562366.0, 8762947.0, "E MTAB 7846:sponge tdr gfp negative rep2 lane1", "0:75.27 1:0", "A:178744772;C:150091912;G:155092318;T:175619332;N:14032", 75, 0, null, null, 178744772, 150091912, 155092318, 175619332, 14032, "ERX3293001", "ERS3358384", "ERA1822647", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.9517, null, 0.06908, null, 0.70822, null, 0.48025, null, 73, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Unknown", "2019-04-08", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9660, "ERR3266385", "ERX3293001", "ERS3358384", "ERP114712", "PRJEB32081", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E-MTAB-7846", "Transcriptome Analysis", "To investigate the activity of sponge enhancers in vertebrates transgenic experiments was performed where sponge enhancers were inserted into zebrafish embryos and stable lines generated abstract: Transcription factors TFs bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs the evolution of enhancers has been difficult to trace because of their fast evolution. Here we take enhancers in the sponge Amphimedon queenslandica and test their activity in zebrafish and mouse. Of the five sponge enhancers assessed three were located in conserved syntenic gene regions that are unique to animals Islet\u2013Scaper Ccne1\u2013Uri Tdrd3\u2013Diaph3. Despite diverging over 700 million yrs ago and a dearth of sequence identity sponge enhancers are able to drive cell type specific reporter gene expression in vertebrates. Analysis of the type and frequency of TF binding motifs in the sponge Islet enhancer allowed for the identification of homologous enhancers in human and mouse which show remarkably similar reporter expression patterns to the sponge enhancer. These findings uncover an unexpected deep conservation of enhancers and suggest that enhancers established early in metazoan evolution can remain functional through retention of combinations of transcription factor binding motifs despite substantial sequence divergence.", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", null, "Protocols: 72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "sponge tdr gfp negative rep2", "SAMEA5556344", "UQ", "ENA FIRST PUBLIC:2019 11 30T04:02:56Z|ENA LAST UPDATE:2019 04 08T12:20:25Z|External Id:SAMEA5556344|INSDC center name:UQ|INSDC first public:2019 11 30T04:02:56Z|INSDC last update:2019 04 08T12:20:25Z|INSDC status:public|Submitter Id:E MTAB 7846:sponge tdr gfp negative rep2|age:72|broker name:ArrayExpress|cell type:GFP negative|common name:zebrafish|developmental stage:larval protruding mouth|genotype:Tgstdrd3 diaph3:eGFPuq7mf|individual:pool 6|organism part:zebrafish comp1nt|sample name:E MTAB 7846:sponge tdr gfp negative rep2|scientific name:Danio rerio|sex:both|strain:A/B or Tu strains", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E MTAB 7846:sponge tdr gfp negative rep2 s", "sponge tdr gfp negative rep2 s", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "Experimental Factor: genotype:Tgstdrd3 diaph3:eGFPuq7mf|Experimental Factor: cell type:GFP negative", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP114712", "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", "E9_9neg_S1_L002_R1_001.fastq.gz", "fastq", 658688825.0, 8751176.0, "E MTAB 7846:sponge tdr gfp negative rep2 lane2", "0:75.27 1:0", "A:178540155;C:149844100;G:154850294;T:175438757;N:15519", 75, 0, null, null, 178540155, 149844100, 154850294, 175438757, 15519, "ERX3293001", "ERS3358384", "ERA1822647", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.95059, null, 0.06748, null, 0.70806, null, 0.48177, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Unknown", "2019-04-08", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9661, "ERR3266386", "ERX3293001", "ERS3358384", "ERP114712", "PRJEB32081", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E-MTAB-7846", "Transcriptome Analysis", "To investigate the activity of sponge enhancers in vertebrates transgenic experiments was performed where sponge enhancers were inserted into zebrafish embryos and stable lines generated abstract: Transcription factors TFs bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs the evolution of enhancers has been difficult to trace because of their fast evolution. Here we take enhancers in the sponge Amphimedon queenslandica and test their activity in zebrafish and mouse. Of the five sponge enhancers assessed three were located in conserved syntenic gene regions that are unique to animals Islet\u2013Scaper Ccne1\u2013Uri Tdrd3\u2013Diaph3. Despite diverging over 700 million yrs ago and a dearth of sequence identity sponge enhancers are able to drive cell type specific reporter gene expression in vertebrates. Analysis of the type and frequency of TF binding motifs in the sponge Islet enhancer allowed for the identification of homologous enhancers in human and mouse which show remarkably similar reporter expression patterns to the sponge enhancer. These findings uncover an unexpected deep conservation of enhancers and suggest that enhancers established early in metazoan evolution can remain functional through retention of combinations of transcription factor binding motifs despite substantial sequence divergence.", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", null, "Protocols: 72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "sponge tdr gfp negative rep2", "SAMEA5556344", "UQ", "ENA FIRST PUBLIC:2019 11 30T04:02:56Z|ENA LAST UPDATE:2019 04 08T12:20:25Z|External Id:SAMEA5556344|INSDC center name:UQ|INSDC first public:2019 11 30T04:02:56Z|INSDC last update:2019 04 08T12:20:25Z|INSDC status:public|Submitter Id:E MTAB 7846:sponge tdr gfp negative rep2|age:72|broker name:ArrayExpress|cell type:GFP negative|common name:zebrafish|developmental stage:larval protruding mouth|genotype:Tgstdrd3 diaph3:eGFPuq7mf|individual:pool 6|organism part:zebrafish comp1nt|sample name:E MTAB 7846:sponge tdr gfp negative rep2|scientific name:Danio rerio|sex:both|strain:A/B or Tu strains", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E MTAB 7846:sponge tdr gfp negative rep2 s", "sponge tdr gfp negative rep2 s", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "Experimental Factor: genotype:Tgstdrd3 diaph3:eGFPuq7mf|Experimental Factor: cell type:GFP negative", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP114712", "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", "E9_9neg_S1_L003_R1_001.fastq.gz", "fastq", 665901310.0, 8846927.0, "E MTAB 7846:sponge tdr gfp negative rep2 lane3", "0:75.27 1:0", "A:180412445;C:151589489;G:156677030;T:177206192;N:16154", 75, 0, null, null, 180412445, 151589489, 156677030, 177206192, 16154, "ERX3293001", "ERS3358384", "ERA1822647", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.95095, null, 0.06855, null, 0.7082, null, 0.4787, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Unknown", "2019-04-08", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9662, "ERR3266387", "ERX3293001", "ERS3358384", "ERP114712", "PRJEB32081", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E-MTAB-7846", "Transcriptome Analysis", "To investigate the activity of sponge enhancers in vertebrates transgenic experiments was performed where sponge enhancers were inserted into zebrafish embryos and stable lines generated abstract: Transcription factors TFs bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs the evolution of enhancers has been difficult to trace because of their fast evolution. Here we take enhancers in the sponge Amphimedon queenslandica and test their activity in zebrafish and mouse. Of the five sponge enhancers assessed three were located in conserved syntenic gene regions that are unique to animals Islet\u2013Scaper Ccne1\u2013Uri Tdrd3\u2013Diaph3. Despite diverging over 700 million yrs ago and a dearth of sequence identity sponge enhancers are able to drive cell type specific reporter gene expression in vertebrates. Analysis of the type and frequency of TF binding motifs in the sponge Islet enhancer allowed for the identification of homologous enhancers in human and mouse which show remarkably similar reporter expression patterns to the sponge enhancer. These findings uncover an unexpected deep conservation of enhancers and suggest that enhancers established early in metazoan evolution can remain functional through retention of combinations of transcription factor binding motifs despite substantial sequence divergence.", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", null, "Protocols: 72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "sponge tdr gfp negative rep2", "SAMEA5556344", "UQ", "ENA FIRST PUBLIC:2019 11 30T04:02:56Z|ENA LAST UPDATE:2019 04 08T12:20:25Z|External Id:SAMEA5556344|INSDC center name:UQ|INSDC first public:2019 11 30T04:02:56Z|INSDC last update:2019 04 08T12:20:25Z|INSDC status:public|Submitter Id:E MTAB 7846:sponge tdr gfp negative rep2|age:72|broker name:ArrayExpress|cell type:GFP negative|common name:zebrafish|developmental stage:larval protruding mouth|genotype:Tgstdrd3 diaph3:eGFPuq7mf|individual:pool 6|organism part:zebrafish comp1nt|sample name:E MTAB 7846:sponge tdr gfp negative rep2|scientific name:Danio rerio|sex:both|strain:A/B or Tu strains", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E MTAB 7846:sponge tdr gfp negative rep2 s", "sponge tdr gfp negative rep2 s", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "Experimental Factor: genotype:Tgstdrd3 diaph3:eGFPuq7mf|Experimental Factor: cell type:GFP negative", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP114712", "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", "E9_9neg_S1_L004_R1_001.fastq.gz", "fastq", 655674573.0, 8711278.0, "E MTAB 7846:sponge tdr gfp negative rep2 lane4", "0:75.27 1:0", "A:177658097;C:149188009;G:154201531;T:174609176;N:17760", 75, 0, null, null, 177658097, 149188009, 154201531, 174609176, 17760, "ERX3293001", "ERS3358384", "ERA1822647", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.9503, null, 0.06838, null, 0.70926, null, 0.47475, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Unknown", "2019-04-08", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9663, "ERR3266380", "ERX3293000", "ERS3358383", "ERP114712", "PRJEB32081", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E-MTAB-7846", "Transcriptome Analysis", "To investigate the activity of sponge enhancers in vertebrates transgenic experiments was performed where sponge enhancers were inserted into zebrafish embryos and stable lines generated abstract: Transcription factors TFs bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs the evolution of enhancers has been difficult to trace because of their fast evolution. Here we take enhancers in the sponge Amphimedon queenslandica and test their activity in zebrafish and mouse. Of the five sponge enhancers assessed three were located in conserved syntenic gene regions that are unique to animals Islet\u2013Scaper Ccne1\u2013Uri Tdrd3\u2013Diaph3. Despite diverging over 700 million yrs ago and a dearth of sequence identity sponge enhancers are able to drive cell type specific reporter gene expression in vertebrates. Analysis of the type and frequency of TF binding motifs in the sponge Islet enhancer allowed for the identification of homologous enhancers in human and mouse which show remarkably similar reporter expression patterns to the sponge enhancer. These findings uncover an unexpected deep conservation of enhancers and suggest that enhancers established early in metazoan evolution can remain functional through retention of combinations of transcription factor binding motifs despite substantial sequence divergence.", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", null, "Protocols: 72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "sponge tdr gfp negative rep1", "SAMEA5556343", "UQ", "ENA FIRST PUBLIC:2019 11 30T04:02:56Z|ENA LAST UPDATE:2019 04 08T12:20:25Z|External Id:SAMEA5556343|INSDC center name:UQ|INSDC first public:2019 11 30T04:02:56Z|INSDC last update:2019 04 08T12:20:25Z|INSDC status:public|Submitter Id:E MTAB 7846:sponge tdr gfp negative rep1|age:72|broker name:ArrayExpress|cell type:GFP negative|common name:zebrafish|developmental stage:larval protruding mouth|genotype:Tgstdrd3 diaph3:eGFPuq7mf|individual:pool 5|organism part:zebrafish comp1nt|sample name:E MTAB 7846:sponge tdr gfp negative rep1|scientific name:Danio rerio|sex:both|strain:A/B or Tu strains", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E MTAB 7846:sponge tdr gfp negative rep1 s", "sponge tdr gfp negative rep1 s", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "Experimental Factor: genotype:Tgstdrd3 diaph3:eGFPuq7mf|Experimental Factor: cell type:GFP negative", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP114712", "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", "E9_6neg_S3_L001_R1_001.fastq.gz", "fastq", 634491637.0, 8440052.0, "E MTAB 7846:sponge tdr gfp negative rep1 lane1", "0:75.18 1:0", "A:170881257;C:145535643;G:150561786;T:167495156;N:17795", 75, 0, null, null, 170881257, 145535643, 150561786, 167495156, 17795, "ERX3293000", "ERS3358383", "ERA1822647", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.94996, null, 0.05672, null, 0.70571, null, 0.48691, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Unknown", "2019-04-08", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9664, "ERR3266381", "ERX3293000", "ERS3358383", "ERP114712", "PRJEB32081", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E-MTAB-7846", "Transcriptome Analysis", "To investigate the activity of sponge enhancers in vertebrates transgenic experiments was performed where sponge enhancers were inserted into zebrafish embryos and stable lines generated abstract: Transcription factors TFs bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs the evolution of enhancers has been difficult to trace because of their fast evolution. Here we take enhancers in the sponge Amphimedon queenslandica and test their activity in zebrafish and mouse. Of the five sponge enhancers assessed three were located in conserved syntenic gene regions that are unique to animals Islet\u2013Scaper Ccne1\u2013Uri Tdrd3\u2013Diaph3. Despite diverging over 700 million yrs ago and a dearth of sequence identity sponge enhancers are able to drive cell type specific reporter gene expression in vertebrates. Analysis of the type and frequency of TF binding motifs in the sponge Islet enhancer allowed for the identification of homologous enhancers in human and mouse which show remarkably similar reporter expression patterns to the sponge enhancer. These findings uncover an unexpected deep conservation of enhancers and suggest that enhancers established early in metazoan evolution can remain functional through retention of combinations of transcription factor binding motifs despite substantial sequence divergence.", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", null, "Protocols: 72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "sponge tdr gfp negative rep1", "SAMEA5556343", "UQ", "ENA FIRST PUBLIC:2019 11 30T04:02:56Z|ENA LAST UPDATE:2019 04 08T12:20:25Z|External Id:SAMEA5556343|INSDC center name:UQ|INSDC first public:2019 11 30T04:02:56Z|INSDC last update:2019 04 08T12:20:25Z|INSDC status:public|Submitter Id:E MTAB 7846:sponge tdr gfp negative rep1|age:72|broker name:ArrayExpress|cell type:GFP negative|common name:zebrafish|developmental stage:larval protruding mouth|genotype:Tgstdrd3 diaph3:eGFPuq7mf|individual:pool 5|organism part:zebrafish comp1nt|sample name:E MTAB 7846:sponge tdr gfp negative rep1|scientific name:Danio rerio|sex:both|strain:A/B or Tu strains", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E MTAB 7846:sponge tdr gfp negative rep1 s", "sponge tdr gfp negative rep1 s", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "Experimental Factor: genotype:Tgstdrd3 diaph3:eGFPuq7mf|Experimental Factor: cell type:GFP negative", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP114712", "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", "E9_6neg_S3_L002_R1_001.fastq.gz", "fastq", 632900752.0, 8418846.0, "E MTAB 7846:sponge tdr gfp negative rep1 lane2", "0:75.18 1:0", "A:170454908;C:145141392;G:150172752;T:167112562;N:19138", 75, 0, null, null, 170454908, 145141392, 150172752, 167112562, 19138, "ERX3293000", "ERS3358383", "ERA1822647", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.94905, null, 0.05627, null, 0.70457, null, 0.4865, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Unknown", "2019-04-08", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [9665, "ERR3266382", "ERX3293000", "ERS3358383", "ERP114712", "PRJEB32081", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E-MTAB-7846", "Transcriptome Analysis", "To investigate the activity of sponge enhancers in vertebrates transgenic experiments was performed where sponge enhancers were inserted into zebrafish embryos and stable lines generated abstract: Transcription factors TFs bind DNA enhancer sequences to regulate gene transcription in animals. Unlike TFs the evolution of enhancers has been difficult to trace because of their fast evolution. Here we take enhancers in the sponge Amphimedon queenslandica and test their activity in zebrafish and mouse. Of the five sponge enhancers assessed three were located in conserved syntenic gene regions that are unique to animals Islet\u2013Scaper Ccne1\u2013Uri Tdrd3\u2013Diaph3. Despite diverging over 700 million yrs ago and a dearth of sequence identity sponge enhancers are able to drive cell type specific reporter gene expression in vertebrates. Analysis of the type and frequency of TF binding motifs in the sponge Islet enhancer allowed for the identification of homologous enhancers in human and mouse which show remarkably similar reporter expression patterns to the sponge enhancer. These findings uncover an unexpected deep conservation of enhancers and suggest that enhancers established early in metazoan evolution can remain functional through retention of combinations of transcription factor binding motifs despite substantial sequence divergence.", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", null, "Protocols: 72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "sponge tdr gfp negative rep1", "SAMEA5556343", "UQ", "ENA FIRST PUBLIC:2019 11 30T04:02:56Z|ENA LAST UPDATE:2019 04 08T12:20:25Z|External Id:SAMEA5556343|INSDC center name:UQ|INSDC first public:2019 11 30T04:02:56Z|INSDC last update:2019 04 08T12:20:25Z|INSDC status:public|Submitter Id:E MTAB 7846:sponge tdr gfp negative rep1|age:72|broker name:ArrayExpress|cell type:GFP negative|common name:zebrafish|developmental stage:larval protruding mouth|genotype:Tgstdrd3 diaph3:eGFPuq7mf|individual:pool 5|organism part:zebrafish comp1nt|sample name:E MTAB 7846:sponge tdr gfp negative rep1|scientific name:Danio rerio|sex:both|strain:A/B or Tu strains", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "E MTAB 7846:sponge tdr gfp negative rep1 s", "sponge tdr gfp negative rep1 s", "RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "72hpf zebrafish embryos were anesthetised with tricane diluted 1:1 in the embryo medium and the yolks were mechanically removed by pipetting up and down at least 10 times in calcium free ringer's solution. Zebrafish embryos were further digested in PBS containing 0.25% liberase at 28\u00b0C for 5 minutes and a single cell solution was prepared by passing through a 40\u03bcm nylon mesh. Both GFP positive and negative single cells were sorted into Trizol LS reagent Life Technologies respectively with a BD FACSAria Cell Sorter BD Biosciences. RNA was extracted using a Direct zol RNA extraction kit Zymo research. RNA Seq libraries were prepared from purified total RNA using a modified Smart Seq2 protocol developed by Picelli et al. 55. 2 ng of purified total RNA 0.4 ng/\u00b5L was combined with 1 \u00b5L of 10 \u00b5M oligo dT primer /5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies and 1 \u00b5L of dNTP mix 10 mM each; Invitrogen y02256 then the protocol was continued as described ref. 2. Briefly the RNA was reverse transcribed with the Smart Seq2 TSO /5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG Integrated DNA Technologies followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol except for the PCR preamplification where the Smart Seq2 ISPCR primer /5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies was added to a final concentration of 0.25 \u00b5M. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit Illumina FC 131 1096 with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Perkin Elmer LabChip GX with the DNA High Sensitivity Reagent kit Perkin Elmer CLS760672. Libraries were pooled in equimolar ratios.", "Experimental Factor: genotype:Tgstdrd3 diaph3:eGFPuq7mf|Experimental Factor: cell type:GFP negative", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP114712", "NextSeq 500 sequencing; RNA seq of GFP positive and negative fractions of zebrafish transgenic cell lines of sea sponge enhancers", "ENA FIRST PUBLIC:2019 11 30|ENA LAST UPDATE:2019 04 08", "E9_6neg_S3_L003_R1_001.fastq.gz", "fastq", 638530115.0, 8494045.0, "E MTAB 7846:sponge tdr gfp negative rep1 lane3", "0:75.17 1:0", "A:171907482;C:146526309;G:151612209;T:168464163;N:19952", 75, 0, null, null, 171907482, 146526309, 151612209, 168464163, 19952, "ERX3293000", "ERS3358383", "ERA1822647", "European Nucleotide Archive", "European Nucleotide Archive", 1, 0.94919, null, 0.05578, null, 0.70849, null, 0.48073, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Unknown", "2019-04-08", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 4362, "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", 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