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A 8 base indexing sequence TCATTGAG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e8e787c0 a000 11e5 800b 68b59976a382|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing", "SC EXP 18730 4#19", "15565962", "Illumina sequencing of library 15565962  constructed from sample accession ERS1021808 for study accession ERP013756.  This is part of an Illumina multiplexed sequencing run 18730 4.  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This submission includes reads tagged with the sequence TCCAGTCG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP013756", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16", "18730_4#17.cram", "cram", 1240938140.0, 9545678.0, "SC RUN 18730 4#17", "0:55 1:75", "A:302318036;C:249218633;G:246601321;T:442702025;N:98125", 55, 75, null, null, 302318036, 249218633, 246601321, 442702025, 98125, "ERX1481457", "ERS1021806", "ERA620320", "European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.23057, 0.63523, 0.05319, 0.067, 0.95213, 0.86695, 0.69753, 0.68537, 55, 75, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-12-16", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [3163, "ERR1410217", "ERX1481456", "ERS1021805", "ERP013756", "PRJEB12296", "Baseline expression from transcriptional profiling of zebrafish developmental stages 2", "Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling", "ArrayExpress:E ERAD 453", null, null, "ZMP phenotype 128 1 pool4", "SAMEA3714656", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:Cleavage:2 cell   ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714656|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:44Z|INSDC last update:2015 12 16T13:42:06Z|INSDC status:public|Submitter Id:e8ab9030 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a pool of 8 wild type zebrafish embryos from ZMP phenotype 128 clutch 1  collected at cleavage   2 cell stage plus ERCC spike mix 2 Ambion. 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This submission includes reads tagged with the sequence TACTTCGG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP013756", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16", "18730_4#13.cram", "cram", 1039867140.0, 7998978.0, "SC RUN 18730 4#13", "0:55 1:75", "A:252384576;C:218519074;G:206578085;T:362298880;N:86525", 55, 75, null, null, 252384576, 218519074, 206578085, 362298880, 86525, "ERX1481453", "ERS1021802", "ERA620320", "European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.18713, 0.60956, 0.05049, 0.0817, 0.95556, 0.87618, 0.66594, 0.68034, 55, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-12-16", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [3167, "ERR1410213", "ERX1481452", "ERS1021801", "ERP013756", "PRJEB12296", "Baseline expression from transcriptional profiling of zebrafish developmental stages 2", "Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling", "ArrayExpress:E ERAD 453", null, null, "ZMP phenotype 128 1 12", "SAMEA3714652", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:Cleavage:2 cell   ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714652|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:45Z|INSDC last update:2015 12 16T13:42:04Z|INSDC status:public|Submitter Id:e89262e0 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a single wild type zebrafish embryo from ZMP phenotype 128 clutch 1  collected at cleavage   2 cell stage plus ERCC spike mix 2 Ambion. 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This submission includes reads tagged with the sequence TCGAAGTG.", "Transcriptome counting qPCR only", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP013756", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16", "18730_4#9.cram", "cram", 987809940.0, 7598538.0, "SC RUN 18730 4#9", "0:55 1:75", "A:248484130;C:197140774;G:188385871;T:353715305;N:83860", 55, 75, null, null, 248484130, 197140774, 188385871, 353715305, 83860, "ERX1481449", "ERS1021798", "ERA620320", "European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.2215, 0.62639, 0.05009, 0.06362, 0.94959, 0.86689, 0.63702, 0.63984, 55, 75, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-12-16", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [3171, "ERR1410209", "ERX1481448", "ERS1021797", "ERP013756", "PRJEB12296", "Baseline expression from transcriptional profiling of zebrafish developmental stages 2", "Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029", "Transcriptome Analysis", "Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling", "ArrayExpress:E ERAD 453", null, null, "ZMP phenotype 128 1 8", "SAMEA3714648", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:Cleavage:2 cell   ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714648|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:44Z|INSDC last update:2015 12 16T13:42:02Z|INSDC status:public|Submitter Id:e87d5440 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a single wild type zebrafish embryo from ZMP phenotype 128 clutch 1  collected at cleavage   2 cell stage plus ERCC spike mix 2 Ambion. 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The sample has been DNAse treated.|sample name:741d9540 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired end sequencing", "SC EXP 19850 2#67", "16564936", "Illumina sequencing of library 16564936  constructed from sample accession ERS1079216 for study accession ERP014517.  This is part of an Illumina multiplexed sequencing run 19850 2.  This submission includes reads tagged with the sequence TACCACCA.", "RNA seq dUTP eukaryotic", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP014517", "Illumina HiSeq 2500 paired end sequencing", "ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16", "19850_2#67.cram", "cram", 331952200.0, 1659761.0, "SC RUN 19850 2#67", "0:100 1:100", "A:88872903;C:76957606;G:77065688;T:88935012;N:120991", 100, 100, null, null, 88872903, 76957606, 77065688, 88935012, 120991, "ERX1513094", "ERS1079216", "ERA648700", "European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.96191, 0.96393, 0.11342, 0.11468, 0.799, 0.79908, 0.58219, 0.58045, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-03-10", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [3972, "ERR1442716", "ERX1513093", "ERS1079215", "ERP014517", "PRJEB12982", "Baseline expression from transcriptional profiling of zebrafish developmental stages 3", "Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130", "Transcriptome Analysis", "RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling", "ArrayExpress:E ERAD 475", null, null, "ZMP phenotype 128 B", "SAMEA3892081", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:Cleavage:2 cell   ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892081|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:05Z|INSDC status:public|Submitter Id:74118750 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:74118750 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired end sequencing", "SC EXP 19850 2#66", "16564924", "Illumina sequencing of library 16564924  constructed from sample accession ERS1079215 for study accession ERP014517.  This is part of an Illumina multiplexed sequencing run 19850 2.  This submission includes reads tagged with the sequence TGAAGCCA.", "RNA seq dUTP eukaryotic", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP014517", "Illumina HiSeq 2500 paired end sequencing", "ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16", "19850_2#66.cram", "cram", 333024200.0, 1665121.0, "SC RUN 19850 2#66", "0:100 1:100", "A:88172616;C:78454066;G:78393792;T:87885914;N:117812", 100, 100, null, null, 88172616, 78454066, 78393792, 87885914, 117812, "ERX1513093", "ERS1079215", "ERA648700", "European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.96249, 0.96556, 0.1289, 0.13166, 0.79945, 0.79961, 0.58336, 0.58063, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-03-10", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [4058, "ERR1442630", "ERX1513007", "ERS1079219", "ERP014517", "PRJEB12982", "Baseline expression from transcriptional profiling of zebrafish developmental stages 3", "Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130", "Transcriptome Analysis", "RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling", "ArrayExpress:E ERAD 475", null, null, "ZMP phenotype 128 F", "SAMEA3892085", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:Cleavage:2 cell   ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892085|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:07Z|INSDC status:public|Submitter Id:744149e0 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:744149e0 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired end sequencing", "SC EXP 19850 1#70", "16564972", "Illumina sequencing of library 16564972  constructed from sample accession ERS1079219 for study accession ERP014517.  This is part of an Illumina multiplexed sequencing run 19850 1.  This submission includes reads tagged with the sequence GATCTCTT.", "RNA seq dUTP eukaryotic", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP014517", "Illumina HiSeq 2500 paired end sequencing", "ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16", "19850_1#70.cram", "cram", 371578800.0, 1857894.0, "SC RUN 19850 1#70", "0:100 1:100", "A:98533022;C:87264222;G:87555118;T:98151909;N:74529", 100, 100, null, null, 98533022, 87264222, 87555118, 98151909, 74529, "ERX1513007", "ERS1079219", "ERA648700", "European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.9636, 0.96761, 0.09699, 0.09916, 0.79525, 0.79553, 0.58618, 0.57988, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-03-10", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [4059, "ERR1442629", "ERX1513006", "ERS1079218", "ERP014517", "PRJEB12982", "Baseline expression from transcriptional profiling of zebrafish developmental stages 3", "Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130", "Transcriptome Analysis", "RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling", "ArrayExpress:E ERAD 475", null, null, "ZMP phenotype 128 E", "SAMEA3892084", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:Cleavage:2 cell   ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892084|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:06Z|INSDC status:public|Submitter Id:74358a10 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:74358a10 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired end sequencing", "SC EXP 19850 1#69", "16564960", "Illumina sequencing of library 16564960  constructed from sample accession ERS1079218 for study accession ERP014517.  This is part of an Illumina multiplexed sequencing run 19850 1.  This submission includes reads tagged with the sequence GGTGAGTT.", "RNA seq dUTP eukaryotic", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP014517", "Illumina HiSeq 2500 paired end sequencing", "ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16", "19850_1#69.cram", "cram", 318342200.0, 1591711.0, "SC RUN 19850 1#69", "0:100 1:100", "A:83801083;C:75621628;G:75578752;T:83271737;N:69000", 100, 100, null, null, 83801083, 75621628, 75578752, 83271737, 69000, "ERX1513006", "ERS1079218", "ERA648700", "European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.96351, 0.96877, 0.10486, 0.10713, 0.79423, 0.79444, 0.57288, 0.57375, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-03-10", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [4060, "ERR1442628", "ERX1513005", "ERS1079217", "ERP014517", "PRJEB12982", "Baseline expression from transcriptional profiling of zebrafish developmental stages 3", "Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130", "Transcriptome Analysis", "RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling", "ArrayExpress:E ERAD 475", null, null, "ZMP phenotype 128 D", "SAMEA3892083", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:Cleavage:2 cell   ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892083|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:06Z|INSDC status:public|Submitter Id:74295510 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:74295510 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired end sequencing", "SC EXP 19850 1#68", "16564948", "Illumina sequencing of library 16564948  constructed from sample accession ERS1079217 for study accession ERP014517.  This is part of an Illumina multiplexed sequencing run 19850 1.  This submission includes reads tagged with the sequence TGCGTGAA.", "RNA seq dUTP eukaryotic", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP014517", "Illumina HiSeq 2500 paired end sequencing", "ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16", "19850_1#68.cram", "cram", 334846000.0, 1674230.0, "SC RUN 19850 1#68", "0:100 1:100", "A:88989528;C:78413149;G:78541907;T:88833028;N:68388", 100, 100, null, null, 88989528, 78413149, 78541907, 88833028, 68388, "ERX1513005", "ERS1079217", "ERA648700", "European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.96197, 0.96681, 0.10873, 0.11111, 0.79805, 0.7992, 0.57474, 0.57198, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-03-10", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [4061, "ERR1442627", "ERX1513004", "ERS1079216", "ERP014517", "PRJEB12982", "Baseline expression from transcriptional profiling of zebrafish developmental stages 3", "Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130", "Transcriptome Analysis", "RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling", "ArrayExpress:E ERAD 475", null, null, "ZMP phenotype 128 C", "SAMEA3892082", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:Cleavage:2 cell   ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892082|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:06Z|INSDC status:public|Submitter Id:741d9540 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:741d9540 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired end sequencing", "SC EXP 19850 1#67", "16564936", "Illumina sequencing of library 16564936  constructed from sample accession ERS1079216 for study accession ERP014517.  This is part of an Illumina multiplexed sequencing run 19850 1.  This submission includes reads tagged with the sequence TACCACCA.", "RNA seq dUTP eukaryotic", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP014517", "Illumina HiSeq 2500 paired end sequencing", "ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16", "19850_1#67.cram", "cram", 332077800.0, 1660389.0, "SC RUN 19850 1#67", "0:100 1:100", "A:88958890;C:76946124;G:77079866;T:89022508;N:70412", 100, 100, null, null, 88958890, 76946124, 77079866, 89022508, 70412, "ERX1513004", "ERS1079216", "ERA648700", "European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.96162, 0.96369, 0.11367, 0.11586, 0.7992, 0.79855, 0.58505, 0.58088, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-03-10", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [4062, "ERR1442626", "ERX1513003", "ERS1079215", "ERP014517", "PRJEB12982", "Baseline expression from transcriptional profiling of zebrafish developmental stages 3", "Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130", "Transcriptome Analysis", "RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling", "ArrayExpress:E ERAD 475", null, null, "ZMP phenotype 128 B", "SAMEA3892081", "Wellcome Sanger Institute", "ArrayExpress DevelopmentalStage:Cleavage:2 cell   ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892081|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:05Z|INSDC status:public|Submitter Id:74118750 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:74118750 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 paired end sequencing", "SC EXP 19850 1#66", "16564924", "Illumina sequencing of library 16564924  constructed from sample accession ERS1079215 for study accession ERP014517.  This is part of an Illumina multiplexed sequencing run 19850 1.  This submission includes reads tagged with the sequence TGAAGCCA.", "RNA seq dUTP eukaryotic", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP014517", "Illumina HiSeq 2500 paired end sequencing", "ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16", "19850_1#66.cram", "cram", 332776400.0, 1663882.0, "SC RUN 19850 1#66", "0:100 1:100", "A:88108657;C:78400833;G:78371292;T:87823689;N:71929", 100, 100, null, null, 88108657, 78400833, 78371292, 87823689, 71929, "ERX1513003", "ERS1079215", "ERA648700", "European Nucleotide Archive", "Wellcome Sanger Institute", 2, 0.96154, 0.96535, 0.12909, 0.13161, 0.79815, 0.79959, 0.58756, 0.58417, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2016-03-10", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [8055, "ERR022484", "ERX008924", "ERS017427", "ERP000400", "PRJEB2333", "Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer", "E-MTAB-434", "Other", null, null, null, null, "E MTAB 434:ZF 2cells", "SAMEA898400", "Wellcome Sanger Institute", "Alias:E MTAB 434:ZF 2cells|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 03 10T17:55:05Z|INSDC last update:2018 03 08T15:25:14Z|INSDC status:public|SRA accession:ERS017427|Sample Name:ERS017427|Sex:mixed|StrainOrLine:Tuebingen|Title:ZF 2cells", null, null, null, null, null, null, null, null, "Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer", "E MTAB 434:sequencing of Zebrafish embryo 2cells", "RNA from Zebrafish embryo 2cells", "Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer", "Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down.   The libraries have fragment size of 250 to 300 bp.", "Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:cell", "FL-cDNA", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer II", null, "ERP000400", "Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer", "ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16", "4946_5.srf", "srf", 3947547008.0, 25970704.0, "E MTAB 434:4946 5.srf", "0:76 1:76", "A:1069302461;C:914233601;G:902631356;T:1055986090;N:5393500", 76, 76, null, null, 1069302461, 914233601, 902631356, 1055986090, 5393500, "ERX008924", "ERS017427", "ERA015179", "SC|Wellcome Trust Sanger Institute", "SC|Wellcome Trust Sanger Institute", 2, 0.93356, 0.93346, 0.03988, 0.04022, 0.79135, 0.79198, 0.48864, 0.48464, 76, 76, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2011-03-10", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [8090, "ERR034125", "ERX012651", "ERS032266", "ERP000635", "PRJEB2512", "The Zebrafish transcriptome during early development", "KI-BN-JKE-DRERIO-RNASEQ-2011", "Transcriptome Analysis", "Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65%   73% reads were successfully mapped to the zebrafish genome and 36%   44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding  protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results  and to further investigate the developmental expression of specific genes  the transcript levels of a subset of genes were analyzed using TaqMan\u00ae array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels  with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes  whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes  number of uniquely expressed genes and enrichment of GO molecular functions.", null, null, "RNA extracted from zebrafish embryo at 16 cell stage", "zebrafish embryo 16 cell", "SAMEA791631", "Department of Biosciences and Nutrition, Karolinska Institutet, Sweden", "ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791631|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition  Karolinska Institutet  Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 16cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 16cell|sex:mixed|strain:Tuebingen", null, null, null, null, null, null, null, null, "Transcriptome profiling of early zebrafish development", "KI BN JKE DRERIO RNASEQ 2011 16cell", "JKE Drerio rna seq", "Transcriptome profiling of 16 cell stage of zebrafish embryos.", "Total RNA was extracted from approximately 150 embryos                     per developmental stage using Trireagent                     Sigma Aldrich. The total RNA was then processed                     further according to the Small RNA Expression Kit                     Applied Biosystems.", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP000635", "AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development", "ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16", "KI-BN-JKE-DRERIO-RNASEQ-2011-16cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-16cell_QV.qual.gz", "SOLiD_native SOLiD_native", 4256756500.0, 85135130.0, "KI BN JKE DRERIO RNASEQ 2011 16cell", "0:50", null, 50, null, null, null, null, null, null, null, null, "ERX012651", "ERS032266", "ERA029959", "KI-BN|Department of Biosciences and Nutrition", "Department of Biosciences and Nutrition, Karolinska Institutet, Sweden", 1, 0.57946, null, 0.08115, null, 0.91896, null, 0.72164, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Sweden", "2011-06-09", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [9296, "ERR202508", "ERX177193", "ERS092407", "ERP001280", "PRJEB2925", "maternal to Zygotic Transition", "maternal_to_Zygotic_Transition-sc-2012-03-12T11:38:43Z-599", "Transcriptome Analysis", "During early stages of embryonic development the genome is transcriptionally inactive and cells are under the control of maternally provided mRNA and proteins. At a key point in development  known as the maternal to zygotic transition MZT  the genome becomes activated and the maternally provided mRNAs begin to degrade. We plan to map the mRNA profiles of genes during the maternal to zygotic transition by using solexa sequencing.", null, null, null, null, "SAMEA1570569", "SC", "ArrayExpress DevelopmentalStage:2 cell|ArrayExpress Genotype:T/LF|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Phenotype:WT|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2012 11 28T14:59:05Z|ENA LAST UPDATE:2018 03 08T15:36:29Z|External Id:SAMEA1570569|INSDC center name:SC|INSDC first public:2012 11 28T14:59:05Z|INSDC last update:2018 03 08T15:36:29Z|INSDC status:public|Submitter Id:2C TotRNA sc 2012 02 06T13:12:17Z 1121923|common name:zebrafish|sample description:RNA seq|sample name:2C TotRNA sc 2012 02 06T13:12:17Z 1121923|scientific name:Danio rerio|strain:T/LF", null, null, null, null, null, null, null, null, "1", "SC EXP 6683 2", "2532385", "Illumina sequencing of library 2532385  constructed from sample accession ERS092407 for study accession ERP001280.", "Illumina cDNA protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP001280", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2012 11 28|ENA LAST UPDATE:2018 11 16", "6683_2.bam", "bam", 11463941550.0, 76426277.0, "SC RUN 6683 2", "0:75 1:75", "A:2384324967;C:3291391074;G:3291238330;T:2457078635;N:39908544", 75, 75, null, null, 2384324967, 3291391074, 3291238330, 2457078635, 39908544, "ERX177193", "ERS092407", "ERA176708", "SC", "Wellcome Sanger Institute", 2, 0.96484, 0.95918, 0.35968, 0.35526, 0.88404, 0.88485, 0.84949, 0.8524, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2012-11-28", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [9298, "ERR202506", "ERX177191", "ERS092405", "ERP001280", "PRJEB2925", "maternal to Zygotic Transition", "maternal_to_Zygotic_Transition-sc-2012-03-12T11:38:43Z-599", "Transcriptome Analysis", "During early stages of embryonic development the genome is transcriptionally inactive and cells are under the control of maternally provided mRNA and proteins. At a key point in development  known as the maternal to zygotic transition MZT  the genome becomes activated and the maternally provided mRNAs begin to degrade. We plan to map the mRNA profiles of genes during the maternal to zygotic transition by using solexa sequencing.", null, null, null, null, "SAMEA1570534", "SC", "ArrayExpress DevelopmentalStage:16 cell|ArrayExpress Genotype:T/LF|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Phenotype:WT|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2012 11 28T14:59:05Z|ENA LAST UPDATE:2018 03 08T15:36:25Z|External Id:SAMEA1570534|INSDC center name:SC|INSDC first public:2012 11 28T14:59:05Z|INSDC last update:2018 03 08T15:36:25Z|INSDC status:public|Submitter Id:16C stan pro sc 2012 02 06T13:12:14Z 1121921|common name:zebrafish|sample description:RNA seq|sample name:16C stan pro sc 2012 02 06T13:12:14Z 1121921|scientific name:Danio rerio|strain:T/LF", null, null, null, null, null, null, null, null, "1", "SC EXP 6317 5", "2532383", "Illumina sequencing of library 2532383  constructed from sample accession ERS092405 for study accession ERP001280.", "Illumina cDNA protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP001280", "Illumina HiSeq 2000 paired end sequencing", "ENA FIRST PUBLIC:2012 11 28|ENA LAST UPDATE:2018 11 16", "6317_5.bam", "bam", 7092438300.0, 47282922.0, "SC RUN 6317 5", "0:75 1:75", "A:1947926886;C:1582039071;G:1595096528;T:1959471222;N:7904593", 75, 75, null, null, 1947926886, 1582039071, 1595096528, 1959471222, 7904593, "ERX177191", "ERS092405", "ERA176708", "SC", "Wellcome Sanger Institute", 2, 0.90801, 0.90631, 0.0426, 0.04216, 0.78486, 0.78539, 0.4795, 0.47872, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2012-11-28", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [9301, "ERR202503", "ERX177188", "ERS092094", "ERP001280", "PRJEB2925", "maternal to Zygotic Transition", "maternal_to_Zygotic_Transition-sc-2012-03-12T11:38:43Z-599", "Transcriptome Analysis", "During early stages of embryonic development the genome is transcriptionally inactive and cells are under the control of maternally provided mRNA and proteins. At a key point in development  known as the maternal to zygotic transition MZT  the genome becomes activated and the maternally provided mRNAs begin to degrade. We plan to map the mRNA profiles of genes during the maternal to zygotic transition by using solexa sequencing.", null, null, null, null, "SAMEA1570566", "SC", "ArrayExpress DevelopmentalStage:64 cell|ArrayExpress Genotype:SAT/WIK|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Phenotype:WT|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2012 11 28T14:59:05Z|ENA LAST UPDATE:2018 03 08T15:36:31Z|External Id:SAMEA1570566|INSDC center name:SC|INSDC first public:2012 11 28T14:59:05Z|INSDC last update:2018 03 08T15:36:31Z|INSDC status:public|Submitter Id:SAT b sc 2012 02 06T13:05:45Z 998060|common name:zebrafish|sample description:RNA seq|sample name:SAT b sc 2012 02 06T13:05:45Z 998060|scientific name:Danio rerio|strain:SAT", null, null, null, null, null, null, null, null, "1", "SC EXP 5552 6", "1476240", "Illumina sequencing of library 1476240  constructed from sample accession ERS092094 for study accession ERP001280.", "Illumina cDNA protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer II", null, "ERP001280", "Illumina Genome Analyzer II paired end sequencing", "ENA FIRST PUBLIC:2012 11 28|ENA LAST UPDATE:2018 11 16", "5552_6.bam", "bam", 3031861428.0, 28072791.0, "SC RUN 5552 6", "0:54 1:54", "A:827548202;C:685397282;G:689217947;T:827560833;N:2137164", 54, 54, null, null, 827548202, 685397282, 689217947, 827560833, 2137164, "ERX177188", "ERS092094", "ERA176708", "SC", "Wellcome Sanger Institute", 2, 0.88709, 0.8867, 0.04219, 0.04381, 0.76836, 0.76978, 0.48688, 0.48607, 54, 54, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2012-11-28", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [9304, "ERR202500", "ERX177185", "ERS092093", "ERP001280", "PRJEB2925", "maternal to Zygotic Transition", "maternal_to_Zygotic_Transition-sc-2012-03-12T11:38:43Z-599", "Transcriptome Analysis", "During early stages of embryonic development the genome is transcriptionally inactive and cells are under the control of maternally provided mRNA and proteins. At a key point in development  known as the maternal to zygotic transition MZT  the genome becomes activated and the maternally provided mRNAs begin to degrade. We plan to map the mRNA profiles of genes during the maternal to zygotic transition by using solexa sequencing.", null, null, null, null, "SAMEA1570541", "SC", "ArrayExpress DevelopmentalStage:2 cell|ArrayExpress Genotype:SAT/WIK|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Phenotype:WT|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2012 11 28T14:59:05Z|ENA LAST UPDATE:2018 03 08T15:36:13Z|External Id:SAMEA1570541|INSDC center name:SC|INSDC first public:2012 11 28T14:59:05Z|INSDC last update:2018 03 08T15:36:13Z|INSDC status:public|Submitter Id:SAT a sc 2012 02 06T13:05:43Z 998059|common name:zebrafish|sample description:RNA seq|sample name:SAT a sc 2012 02 06T13:05:43Z 998059|scientific name:Danio rerio|strain:SAT", null, null, null, null, null, null, null, null, "1", "SC EXP 5540 7", "1392795", "Illumina sequencing of library 1392795  constructed from sample accession ERS092093 for study accession ERP001280.", "Illumina cDNA protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer II", null, "ERP001280", "Illumina Genome Analyzer II paired end sequencing", "ENA FIRST PUBLIC:2012 11 28|ENA LAST UPDATE:2018 11 16", "5540_7.bam", "bam", 4139896608.0, 38332376.0, "SC RUN 5540 7", "0:54 1:54", "A:1123995667;C:935834208;G:933659183;T:1138309303;N:8098247", 54, 54, null, null, 1123995667, 935834208, 933659183, 1138309303, 8098247, "ERX177185", "ERS092093", "ERA176708", "SC", "Wellcome Sanger Institute", 2, 0.89473, 0.89261, 0.0475, 0.0496, 0.80413, 0.80551, 0.49672, 0.49064, 54, 54, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2012-11-28", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [9308, "ERR202496", "ERX177181", "ERS092089", "ERP001280", "PRJEB2925", "maternal to Zygotic Transition", "maternal_to_Zygotic_Transition-sc-2012-03-12T11:38:43Z-599", "Transcriptome Analysis", "During early stages of embryonic development the genome is transcriptionally inactive and cells are under the control of maternally provided mRNA and proteins. At a key point in development  known as the maternal to zygotic transition MZT  the genome becomes activated and the maternally provided mRNAs begin to degrade. We plan to map the mRNA profiles of genes during the maternal to zygotic transition by using solexa sequencing.", null, null, null, null, "SAMEA1570537", "SC", "ArrayExpress DevelopmentalStage:64 cell|ArrayExpress Genotype:WIK/SAT|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Phenotype:WT|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2012 11 28T14:59:05Z|ENA LAST UPDATE:2018 03 08T15:36:15Z|External Id:SAMEA1570537|INSDC center name:SC|INSDC first public:2012 11 28T14:59:05Z|INSDC last update:2018 03 08T15:36:15Z|INSDC status:public|Submitter Id:WIK b sc 2012 02 06T13:05:39Z 998055|common name:zebrafish|sample description:RNA seq|sample name:WIK b sc 2012 02 06T13:05:39Z 998055|scientific name:Danio rerio|strain:WIK", null, null, null, null, null, null, null, null, "1", "SC EXP 5540 2", "1392791", "Illumina sequencing of library 1392791  constructed from sample accession ERS092089 for study accession ERP001280.", "Illumina cDNA protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer II", null, "ERP001280", "Illumina Genome Analyzer II paired end sequencing", "ENA FIRST PUBLIC:2012 11 28|ENA LAST UPDATE:2018 11 16", "5540_2.bam", "bam", 3934066536.0, 36426542.0, "SC RUN 5540 2", "0:54 1:54", "A:1089272408;C:875257818;G:871131618;T:1090449345;N:7955347", 54, 54, null, null, 1089272408, 875257818, 871131618, 1090449345, 7955347, "ERX177181", "ERS092089", "ERA176708", "SC", "Wellcome Sanger Institute", 2, 0.92002, 0.92014, 0.04875, 0.05104, 0.76061, 0.76161, 0.4821, 0.48296, 54, 54, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2012-11-28", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [9309, "ERR202495", "ERX177180", "ERS092088", "ERP001280", "PRJEB2925", "maternal to Zygotic Transition", "maternal_to_Zygotic_Transition-sc-2012-03-12T11:38:43Z-599", "Transcriptome Analysis", "During early stages of embryonic development the genome is transcriptionally inactive and cells are under the control of maternally provided mRNA and proteins. At a key point in development  known as the maternal to zygotic transition MZT  the genome becomes activated and the maternally provided mRNAs begin to degrade. We plan to map the mRNA profiles of genes during the maternal to zygotic transition by using solexa sequencing.", null, null, null, null, "SAMEA1570572", "SC", "ArrayExpress DevelopmentalStage:2 cell|ArrayExpress Genotype:WIK/SAT|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Phenotype:WT|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2012 11 28T14:59:05Z|ENA LAST UPDATE:2018 03 08T15:36:31Z|External Id:SAMEA1570572|INSDC center name:SC|INSDC first public:2012 11 28T14:59:05Z|INSDC last update:2018 03 08T15:36:31Z|INSDC status:public|Submitter Id:WIK a sc 2012 02 06T13:05:37Z 998054|common name:zebrafish|sample description:RNA seq|sample name:WIK a sc 2012 02 06T13:05:37Z 998054|scientific name:Danio rerio|strain:WIK", null, null, null, null, null, null, null, null, "1", "SC EXP 5540 1", "1392790", "Illumina sequencing of library 1392790  constructed from sample accession ERS092088 for study accession ERP001280.", "Illumina cDNA protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer II", null, "ERP001280", "Illumina Genome Analyzer II paired end sequencing", "ENA FIRST PUBLIC:2012 11 28|ENA LAST UPDATE:2018 11 16", "5540_1.bam", "bam", 4120158204.0, 38149613.0, "SC RUN 5540 1", "0:54 1:54", "A:1165514767;C:896704109;G:892695229;T:1156428740;N:8815359", 54, 54, null, null, 1165514767, 896704109, 892695229, 1156428740, 8815359, "ERX177180", "ERS092088", "ERA176708", "SC", "Wellcome Sanger Institute", 2, 0.9228, 0.92241, 0.05498, 0.05795, 0.79091, 0.79235, 0.50034, 0.50151, 54, 54, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2012-11-28", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [9726, "ERR3841993", "ERX3854555", "ERS3555998", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 2", "SAMEA5752539", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752539|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:2|common name:zebrafish|dev stage:64 cell|sample name:2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 3", "64 cell 3", "OTHER", "RNA Seq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14", null, null, 1579307816.0, 20780366.0, "ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 3", "0:76", "A:589876602;C:380048242;G:392473318;T:216893826;N:15828", 76, null, null, null, 589876602, 380048242, 392473318, 216893826, 15828, "ERX3854555", "ERS3555998", "ERA2359305", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.15411, null, 0.04564, null, 0.97883, null, 0.55376, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9727, "ERR3841992", "ERX3854554", "ERS3556003", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 4Ei 10", "SAMEA5752544", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752544|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:7|common name:zebrafish|dev stage:64 cell|sample name:7|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 2", "64 cell 4Ei", "OTHER", "RNA Seq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14", null, null, 1213585480.0, 15968230.0, "ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 2", "0:76", "A:548456563;C:244465528;G:271963808;T:148687764;N:11817", 76, null, null, null, 548456563, 244465528, 271963808, 148687764, 11817, "ERX3854554", "ERS3556003", "ERA2359305", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.21973, null, 0.10926, null, 0.97419, null, 0.44348, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9728, "ERR3841991", "ERX3854553", "ERS3555997", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 1", "SAMEA5752538", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:405 1", "64 cell 1", "OTHER", "RNA Seq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14", null, null, 1494930944.0, 19670144.0, "ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 1", "0:76", "A:543017836;C:366974203;G:367027373;T:217896401;N:15131", 76, null, null, null, 543017836, 366974203, 367027373, 217896401, 15131, "ERX3854553", "ERS3555997", "ERA2359305", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.2544, null, 0.08957, null, 0.96568, null, 0.55681, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9742, "ERR3489868", "ERX3511283", "ERS3556003", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 4Ei 10", "SAMEA5752544", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752544|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:7|common name:zebrafish|dev stage:64 cell|sample name:7|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 20", "64 cell 4Ei 10 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 5928054796.0, 78000721.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 20", "0:76", "A:2109854905;C:1377083508;G:1616166285;T:824889630;N:60468", 76, null, null, null, 2109854905, 1377083508, 1616166285, 824889630, 60468, "ERX3511283", "ERS3556003", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.61525, null, 0.45233, null, 0.99379, null, 0.57373, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9743, "ERR3489867", "ERX3511282", "ERS3556003", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 4Ei 10", "SAMEA5752544", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752544|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:7|common name:zebrafish|dev stage:64 cell|sample name:7|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 19", "64 cell 4Ei 10 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 9772604780.0, 128586905.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 19", "0:76", "A:3901301079;C:2223067879;G:2553338016;T:1094797648;N:100158", 76, null, null, null, 3901301079, 2223067879, 2553338016, 1094797648, 100158, "ERX3511282", "ERS3556003", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.52103, null, 0.25046, null, 0.9861, null, 0.64575, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9744, "ERR3489866", "ERX3511281", "ERS3556002", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 4Ei 0.1", "SAMEA5752543", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752543|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:6|common name:zebrafish|dev stage:64 cell|sample name:6|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 18", "64 cell 4Ei 0.1 LSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 09 26", null, null, 6730725680.0, 88562180.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 18", "0:76", "A:3805722011;C:1188715051;G:1382258076;T:353814168;N:216374", 76, null, null, null, 3805722011, 1188715051, 1382258076, 353814168, 216374, "ERX3511281", "ERS3556002", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.61922, null, 0.37217, null, 0.99527, null, 0.29148, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9745, "ERR3489865", "ERX3511280", "ERS3556002", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 4Ei 0.1", "SAMEA5752543", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752543|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:6|common name:zebrafish|dev stage:64 cell|sample name:6|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 17", "64 cell 4Ei 0.1 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 09 26", null, null, 10616304872.0, 139688222.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 17", "0:76", "A:4717003484;C:2600725234;G:2586105174;T:712124440;N:346540", 76, null, null, null, 4717003484, 2600725234, 2586105174, 712124440, 346540, "ERX3511280", "ERS3556002", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.30908, null, 0.08252, null, 0.94683, null, 0.69548, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9758, "ERR3489852", "ERX3511267", "ERS3555998", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 2", "SAMEA5752539", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752539|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:2|common name:zebrafish|dev stage:64 cell|sample name:2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 4", "64 cell 2 LSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 11722578884.0, 154244459.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 4", "0:76", "A:8175036829;C:1396062240;G:1882846539;T:268587131;N:46145", 76, null, null, null, 8175036829, 1396062240, 1882846539, 268587131, 46145, "ERX3511267", "ERS3555998", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.81133, null, 0.41331, null, 0.99823, null, 0.03453, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9759, "ERR3489851", "ERX3511266", "ERS3555998", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 2", "SAMEA5752539", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752539|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:2|common name:zebrafish|dev stage:64 cell|sample name:2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 3", "64 cell 2 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 9525478088.0, 125335238.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 3", "0:76", "A:4813606784;C:2048902072;G:2140220088;T:522714000;N:35144", 76, null, null, null, 4813606784, 2048902072, 2140220088, 522714000, 35144, "ERX3511266", "ERS3555998", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.59747, null, 0.26784, null, 0.996, null, 0.21193, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9760, "ERR3489850", "ERX3511265", "ERS3555997", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 1", "SAMEA5752538", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 2", "64 cell 1 LSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 8544157652.0, 112423127.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 2", "0:76", "A:2633354802;C:2582123846;G:2505786164;T:822713754;N:179086", 76, null, null, null, 2633354802, 2582123846, 2505786164, 822713754, 179086, "ERX3511265", "ERS3555997", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.34707, null, 0.02129, null, 0.99797, null, 0.62478, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9761, "ERR3489849", "ERX3511264", "ERS3555997", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 1", "SAMEA5752538", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 1", "64 cell 1 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", "run7_64_cell_SSU_12_13_14.fastq.gz", "fastq", 10139466432.0, 133414032.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 1", "0:76 1:0", "A:4628193785;C:2494821868;G:2485640988;T:530605907;N:203884", 76, 0, null, null, 4628193785, 2494821868, 2485640988, 530605907, 203884, "ERX3511264", "ERS3555997", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.06893, null, 0.02559, null, 0.99766, null, 0.90567, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9762, "ERR3413870", "ERX3437516", "ERS3555997", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 1", "SAMEA5752538", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 03 07 2019 14:45:09:705 2", "64 cell 1 LSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, 8544157652.0, 112423127.0, "ena RUN Computational Biology Unit 03 07 2019 14:45:09:705 2", "0:76", "A:2633354802;C:2582123846;G:2505786164;T:822713754;N:179086", 76, null, null, null, 2633354802, 2582123846, 2505786164, 822713754, 179086, "ERX3437516", "ERS3555997", "ERA2028987", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.34696, null, 0.02086, null, 0.99795, null, 0.66261, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9763, "ERR3413869", "ERX3437515", "ERS3555997", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 1", "SAMEA5752538", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 03 07 2019 14:45:09:705 1", "64 cell 1 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, 10139466432.0, 133414032.0, "ena RUN Computational Biology Unit 03 07 2019 14:45:09:705 1", "0:76", "A:4628193785;C:2494821868;G:2485640988;T:530605907;N:203884", 76, null, null, null, 4628193785, 2494821868, 2485640988, 530605907, 203884, "ERX3437515", "ERS3555997", "ERA2028987", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.06884, null, 0.02526, null, 0.99762, null, 0.89856, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9919, "ERR5167510", "ERX4972431", "ERS5593364", "ERP122761", "PRJEB39265", "RNA dynamics during zebrafish development", "ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183", "Other", "RNA dynamics during early zebrafish development", "ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05", null, null, "cDNA WT 2hpf rep1", "JD T20 PDPN191089", null, "ENA FIRST PUBLIC:2022 07 05T12:06:34Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:34Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05", null, null, null, null, null, null, null, null, "PromethION sequencing", "ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 21 01 2021 22:16:50:154 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "OXFORD_NANOPORE", "PromethION", null, "ERP122761", "PromethION sequencing", "ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05", null, null, null, null, "ena RUN CENTER FOR GENOMIC REGULATION CRG 21 01 2021 22:16:50:154 1", null, null, null, null, null, null, null, null, null, null, null, "ERX4972431", null, "ERA3319053", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "ont", "ont", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2022-07-05", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [24550, "ERR964668", "ERX1041631", "ERS792102", "ERP011038", "PRJEB9889", "The Zebrafish transcriptome during early development", "ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22", "Other", "Zebrafish has emerged as a model organism to investigate vertebrate development  and human genetic diseases. However  currently zebrafish annotation is still ongoing and clearly not sufficed  therefore  providing opportunity for novel transcript finding.  With the introduction of massive parallel sequencing  whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study  we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation.", null, null, null, "KI BN JKE DRERIO RNASEQ", "SAMEA3484817", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION", "ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484817|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 16cell|common name:zebrafish|dev stage:16 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 16cell|strain:Tuebingen", null, null, null, null, null, null, null, null, "AB SOLiD System 3.0 sequencing", "ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:870 2", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "ERP011038", "AB SOLiD System 3.0 sequencing", "ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16", "KI-BN-JKE-DRERIO-RNASEQ-20090709-16cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-16cell_F3_QV.qual.gz", "SOLiD_native SOLiD_native", 5278508300.0, 105570166.0, "ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 2", "0:50", "0:1410981717;1:1203936808;2:1415708111;3:1223403795;.:24477869", 50, null, null, null, null, null, null, null, null, "ERX1041631", "ERS792102", "ERA458495", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION", 1, 0.71371, null, 0.09346, null, 0.91539, null, 0.73015, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Sweden", "2015-07-15", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [24553, "ERR964672", "ERX1041635", "ERS792102", "ERP011038", "PRJEB9889", "The Zebrafish transcriptome during early development", "ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22", "Other", "Zebrafish has emerged as a model organism to investigate vertebrate development  and human genetic diseases. However  currently zebrafish annotation is still ongoing and clearly not sufficed  therefore  providing opportunity for novel transcript finding.  With the introduction of massive parallel sequencing  whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study  we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation.", null, null, null, "KI BN JKE DRERIO RNASEQ", "SAMEA3484817", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION", "ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484817|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 16cell|common name:zebrafish|dev stage:16 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 16cell|strain:Tuebingen", null, null, null, null, null, null, null, null, "AB SOLiD System 3.0 sequencing", "ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 6", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "ERP011038", "AB SOLiD System 3.0 sequencing", "ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16", "KI-BN-JKE-DRERIO-RNASEQ-20091014-16cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-16cell_F3_QV.qual.gz", "SOLiD_native SOLiD_native", 2719433200.0, 54388664.0, "ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 6", "0:50", "0:699731678;1:628745158;2:754903505;3:633574679;.:2478180", 50, null, null, null, null, null, null, null, null, "ERX1041635", "ERS792102", "ERA458495", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive", "KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION", 1, 0.73214, null, 0.09566, null, 0.90836, null, 0.74043, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Sweden", "2015-07-15", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [28560, "SRR26395034", "SRX22100899", "SRS19166025", "SRP466518", "PRJNA1028258", "Zygotic activation of transposable elements during zebrafish early embryogenesis", "PRJNA1028258", "Other", "Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.", null, "pubmed:40246845", null, null, "64 cell RNA seq rep8", null, "strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 64 8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Illumina RNA seq of zebrafish: 64 cell replicate8", "DR 035", "DR 035", "mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP466518", null, null, "C64-8_1.fq.gz C64-8_2.fq.gz", "fastq fastq", 13755975120.0, 50948056.0, "C64 8 1.fq.gz", "0:135 1:135", "A:3658420874;C:3226727105;G:3239474262;T:3628930832;N:2422047", 135, 135, null, null, 3658420874, 3226727105, 3239474262, 3628930832, 2422047, "SRX22100899", "SRS19166025", "SRA1731898", "University of Michigan|Computational Medicine and Bioinformatics", "University of Michigan", 2, 0.92463, 0.92386, 0.0253, 0.02389, 0.77441, 0.77851, 0.48196, 0.47927, 135, 135, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-10-16", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28561, "SRR26395035", "SRX22100898", "SRS19166024", "SRP466518", "PRJNA1028258", "Zygotic activation of transposable elements during zebrafish early embryogenesis", "PRJNA1028258", "Other", "Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.", null, "pubmed:40246845", null, null, "64 cell RNA seq rep7", null, "strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 64 7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Illumina RNA seq of zebrafish: 64 cell replicate7", "DR 034", "DR 034", "mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP466518", null, null, "C64-7_1.fq.gz C64-7_2.fq.gz", "fastq fastq", 14250954780.0, 52781314.0, "C64 7 1.fq.gz", "0:135 1:135", "A:3810945650;C:3320623800;G:3339892194;T:3776960886;N:2532250", 135, 135, null, null, 3810945650, 3320623800, 3339892194, 3776960886, 2532250, "SRX22100898", "SRS19166024", "SRA1731898", "University of Michigan|Computational Medicine and Bioinformatics", "University of Michigan", 2, 0.93734, 0.93685, 0.02705, 0.02576, 0.77553, 0.7791, 0.47481, 0.47745, 135, 135, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-10-16", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28562, "SRR26395036", "SRX22100897", "SRS19166023", "SRP466518", "PRJNA1028258", "Zygotic activation of transposable elements during zebrafish early embryogenesis", "PRJNA1028258", "Other", "Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.", null, "pubmed:40246845", null, null, "64 cell RNA seq rep6", null, "strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 64 6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Illumina RNA seq of zebrafish: 64 cell replicate6", "DR 033", "DR 033", "mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP466518", null, null, "C64-6_1.fq.gz C64-6_2.fq.gz", "fastq fastq", 14251193190.0, 52782197.0, "C64 6 1.fq.gz", "0:135 1:135", "A:3801408063;C:3332053069;G:3345233238;T:3769986735;N:2512085", 135, 135, null, null, 3801408063, 3332053069, 3345233238, 3769986735, 2512085, "SRX22100897", "SRS19166023", "SRA1731898", "University of Michigan|Computational Medicine and Bioinformatics", "University of Michigan", 2, 0.94348, 0.94342, 0.02571, 0.02414, 0.77112, 0.77492, 0.48218, 0.4777, 135, 135, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-10-16", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28563, "SRR26395037", "SRX22100896", "SRS19166022", "SRP466518", "PRJNA1028258", "Zygotic activation of transposable elements during zebrafish early embryogenesis", "PRJNA1028258", "Other", "Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.", null, "pubmed:40246845", null, null, "64 cell RNA seq rep5", null, "strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 64 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Illumina RNA seq of zebrafish: 64 cell replicate5", "DR 032", "DR 032", "mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP466518", null, null, "C64-5_1.fq.gz C64-5_2.fq.gz", "fastq fastq", 15142948650.0, 56084995.0, "C64 5 1.fq.gz", "0:135 1:135", "A:4031434744;C:3549307228;G:3562636129;T:3996868396;N:2702153", 135, 135, null, null, 4031434744, 3549307228, 3562636129, 3996868396, 2702153, "SRX22100896", "SRS19166022", "SRA1731898", "University of Michigan|Computational Medicine and Bioinformatics", "University of Michigan", 2, 0.93753, 0.93663, 0.02519, 0.024, 0.77301, 0.77674, 0.47421, 0.46951, 135, 135, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-10-16", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28564, "SRR26395038", "SRX22100895", "SRS19166021", "SRP466518", "PRJNA1028258", "Zygotic activation of transposable elements during zebrafish early embryogenesis", "PRJNA1028258", "Other", "Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.", null, "pubmed:40246845", null, null, "64 cell RNA seq rep4", null, "strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 64 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Illumina RNA seq of zebrafish: 64 cell replicate4", "DR 031", "DR 031", "mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP466518", null, null, "C64-4_1.fq.gz C64-4_2.fq.gz", "fastq fastq", 14488466220.0, 53660986.0, "C64 4 1.fq.gz", "0:135 1:135", "A:3863267905;C:3389148218;G:3402037749;T:3831469669;N:2542679", 135, 135, null, null, 3863267905, 3389148218, 3402037749, 3831469669, 2542679, "SRX22100895", "SRS19166021", "SRA1731898", "University of Michigan|Computational Medicine and Bioinformatics", "University of Michigan", 2, 0.93879, 0.93825, 0.02613, 0.02437, 0.77212, 0.77577, 0.47796, 0.47196, 135, 135, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-10-16", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28566, "SRR26395040", "SRX22100893", "SRS19166019", "SRP466518", "PRJNA1028258", "Zygotic activation of transposable elements during zebrafish early embryogenesis", "PRJNA1028258", "Other", "Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.", null, "pubmed:40246845", null, null, "64 cell RNA seq rep3", null, "strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 64 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Illumina RNA seq of zebrafish: 64 cell replicate3", "DR 030", "DR 030", "mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP466518", null, null, "C64-3_1.fq.gz C64-3_2.fq.gz", "fastq fastq", 16017940620.0, 59325706.0, "C64 3 1.fq.gz", "0:135 1:135", "A:4273558549;C:3744205640;G:3760255830;T:4237074764;N:2845837", 135, 135, null, null, 4273558549, 3744205640, 3760255830, 4237074764, 2845837, "SRX22100893", "SRS19166019", "SRA1731898", "University of Michigan|Computational Medicine and Bioinformatics", "University of Michigan", 2, 0.93688, 0.9383, 0.02702, 0.02595, 0.77433, 0.7767, 0.47319, 0.47413, 135, 135, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-10-16", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28567, "SRR26395041", "SRX22100892", "SRS19166018", "SRP466518", "PRJNA1028258", "Zygotic activation of transposable elements during zebrafish early embryogenesis", "PRJNA1028258", "Other", "Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.", null, "pubmed:40246845", null, null, "64 cell RNA seq rep2", null, "strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 64 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Illumina RNA seq of zebrafish: 64 cell replicate2", "DR 029", "DR 029", "mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP466518", null, null, "C64-2_1.fq.gz C64-2_2.fq.gz", "fastq fastq", 16732836630.0, 61973469.0, "C64 2 1.fq.gz", "0:135 1:135", "A:4451249064;C:3924735460;G:3940154978;T:4413679398;N:3017730", 135, 135, null, null, 4451249064, 3924735460, 3940154978, 4413679398, 3017730, "SRX22100892", "SRS19166018", "SRA1731898", "University of Michigan|Computational Medicine and Bioinformatics", "University of Michigan", 2, 0.94302, 0.94257, 0.02459, 0.02333, 0.77248, 0.77479, 0.47902, 0.47678, 135, 135, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-10-16", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28568, "SRR26395042", "SRX22100891", "SRS19166017", "SRP466518", "PRJNA1028258", "Zygotic activation of transposable elements during zebrafish early embryogenesis", "PRJNA1028258", "Other", "Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.", null, "pubmed:40246845", null, null, "64 cell RNA seq rep1", null, "strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 64 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Illumina RNA seq of zebrafish: 64 cell replicate1", "DR 028", "DR 028", "mRNA from five stages fertilized egg  1 cell  64 cell  1k cell  and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP466518", null, null, "C64-1_1.fq.gz C64-1_2.fq.gz", "fastq fastq", 16459047450.0, 60959435.0, "C64 1 1.fq.gz", "0:135 1:135", "A:4391773658;C:3847087464;G:3866793612;T:4350489494;N:2903222", 135, 135, null, null, 4391773658, 3847087464, 3866793612, 4350489494, 2903222, "SRX22100891", "SRS19166017", "SRA1731898", "University of Michigan|Computational Medicine and Bioinformatics", "University of Michigan", 2, 0.94676, 0.94707, 0.02568, 0.0244, 0.77236, 0.77593, 0.48374, 0.47691, 135, 135, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-10-16", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28576, "SRR26395050", "SRX22100883", "SRS19166009", "SRP466518", "PRJNA1028258", "Zygotic activation of transposable elements during zebrafish early embryogenesis", "PRJNA1028258", "Other", "Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus  transcript  and allele over zebrafish early embryonic development. Moreover  we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish  where extensive variation exists among TE families  subfamilies  loci  transcripts and alleles with respect to evolutionary age.", null, "pubmed:40246845", null, null, "64 cell Iso seq", null, "strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "PacBio Iso seq of zebrafish: 64 cell", "DR 003", "DR 003", "Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN  CA  USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies  CA  USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies  CA  USA. RNA samples with a RIN  8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA  Inc.  Mountain View  CA  USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems  Wilmington  MA  USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently  two cDNA libraries <3 kb  >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences  Menlo Park  CA  USA and sequenced on the PacBio sequel II platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "PACBIO_SMRT", "Sequel", null, "SRP466518", null, null, "cell64_1.ccs.fq.gz cell64_2.ccs.fq.gz", "fastq fastq", 2829660788.0, 1238867.0, "cell64 1.ccs.fq.gz", "0:2284.07", "A:765802910;C:646754322;G:668768985;T:748334571;N:0", 2284, null, null, null, 765802910, 646754322, 668768985, 748334571, 0, "SRX22100883", "SRS19166009", "SRA1731898", "University of Michigan|Computational Medicine and Bioinformatics", "University of Michigan", 1, 0.37504, null, 0.00108, null, 0.91149, null, 0.48939, null, 1913, null, "T", null, "long read", "pacbio", "pacbio_modern", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2023-10-16", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28935, "SRR26845669", "SRX22541151", "SRS19550737", "SRP472252", "PRJNA1040929", "Slam seq reveals that miR 430 regulates zygotic mRNA during zebrafish embryogenesis [timecourse data]", "GSE247933", "Other", "Background: Early embryonic developmental programs are guided by the coordinated interplay between maternally inherited and zygotically manufactured RNAs and proteins. Although these processes happen concomitantly and affecting gene function during this period is bound to affect both pools of mRNAs  it has been challenging to study their expression dynamics separately. Results: By employing Slam seq  a nascent mRNA labeling transcriptomic approach  in a developmental time series we observe that over half of the early zebrafish embryo transcriptome consists of maternal zygotic genes  emphasizing their pivotal role in early embryogenesis. We provide an hourly resolution of de novo transcriptional waves and follow nascent mRNA trajectories  finding that most de novo transcriptional events are stable throughout this period. Additionally  by blocking microRNA430 function  a key post transcriptional regulator during zebrafish embryogenesis  we directly show that it destabilizes hundreds of de novo transcribed mRNAs from pure zygotic as well as maternal zygotic genes. This unveils a novel miR 430 function during embryogenesis  fine tuning zygotic gene expression  which highlights that Slam seq can be used to disentangle transcriptional and post transcriptional regulation of mRNA levels.  Conclusion: Such valuable insights into zebrafish early embryo transcriptome dynamics emphasize the significance of post transcriptional regulators in zygotic genome activation. These findings pave the way for future investigations into the coordinated interplay between transcriptional and post transcriptional landscapes required for the establishment of animal cell identities and functions. Overall design: Zebrafish embryos were dechorionated and injected at single cell stage with 1000pL of 75mM s4 UTP. Embryos were kept in the dark until collection time. Total RNA was extracted  and kept away from direct light   alkylated  used for library preparation with QuantSeq three prime mRNA Seq Library Prep Kit for Illumina FWD.", "parent bioproject:PRJNA1040928", null, null, "zebrafish 2hour wt 75mM s4u r2", "GSM7903257", null, "tissue:Embryos at 2 hpf of [AB TU]x[TL TLF]|geo loc name:missing|collection date:missing", "zebrafish 2hour wt 75mM s4u r2", "Slamdunk 0.4.3. Adapter sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC Reads that contain at least 2 T>C conversions were deemed labeled. Assembly: danRer11 Supplementary files format and content: Comma separated values  <.csv>; Total raw read and labeled read counts for all experiments and samples  including spike ins. Rows represent different three primeUTR isoforms for coding genes or full length transcript non coding genes. Columns represent: Ensembl gene IDs by itself non coding transcripts + three primeUTR isoforms coding transcripts  or ERCC IDs spike ins;  Chromosome name; Genomic start of feature; Genomic end of feature; DNA strand of feature; Number of Ts within feature;", "Embryos at 2 hpf", "Embryos were injected with 1000pL of 75mM s4 UTP.", "Trizol\u2122 QuantSeq 3\u2032 mRNA Seq Library Prep Kit for Illumina UDI Bundle FWD  Lexogen GmbH  cat. no. 144.96", "Zebrafish embryos were collected from natural breeding  with random mating parents  embryos were kept at 28.5 C in 0.5x Embryo Media.", "tissue:Embryos|Stage:2 hpf of [AB TU]x[TL TLF]", "GSM7903257", "GSM7903257: zebrafish 2hour wt 75mM s4u r2; Danio rerio; RNA Seq", "GSM7903257 r1", "GSM7903257", "1", "Trizol\u2122 QuantSeq 3\u2032 mRNA Seq Library Prep Kit for Illumina UDI Bundle FWD  Lexogen GmbH  cat. no. 144.96", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP472252", null, "loader:fastq load.py", "s2h_2.fastq.gz", "fastq", 4440596805.0, 43966305.0, "GSM7903257 r1", "0:101", "A:1543708731;C:806593065;G:905733733;T:1182095254;N:2466022", 101, null, null, null, 1543708731, 806593065, 905733733, 1182095254, 2466022, "SRX22541151", "SRS19550737", "SRA1751928", "Bazzini Lab, Stowers Institute for Medical Research", "Bazzini Lab, Stowers Institute for Medical Research", 1, 0.63778, null, 0.15677, null, 0.82676, null, 0.61166, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2023-11-15", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28936, "SRR26845670", "SRX22541150", "SRS19550735", "SRP472252", "PRJNA1040929", "Slam seq reveals that miR 430 regulates zygotic mRNA during zebrafish embryogenesis [timecourse data]", "GSE247933", "Other", "Background: Early embryonic developmental programs are guided by the coordinated interplay between maternally inherited and zygotically manufactured RNAs and proteins. Although these processes happen concomitantly and affecting gene function during this period is bound to affect both pools of mRNAs  it has been challenging to study their expression dynamics separately. Results: By employing Slam seq  a nascent mRNA labeling transcriptomic approach  in a developmental time series we observe that over half of the early zebrafish embryo transcriptome consists of maternal zygotic genes  emphasizing their pivotal role in early embryogenesis. We provide an hourly resolution of de novo transcriptional waves and follow nascent mRNA trajectories  finding that most de novo transcriptional events are stable throughout this period. Additionally  by blocking microRNA430 function  a key post transcriptional regulator during zebrafish embryogenesis  we directly show that it destabilizes hundreds of de novo transcribed mRNAs from pure zygotic as well as maternal zygotic genes. This unveils a novel miR 430 function during embryogenesis  fine tuning zygotic gene expression  which highlights that Slam seq can be used to disentangle transcriptional and post transcriptional regulation of mRNA levels.  Conclusion: Such valuable insights into zebrafish early embryo transcriptome dynamics emphasize the significance of post transcriptional regulators in zygotic genome activation. These findings pave the way for future investigations into the coordinated interplay between transcriptional and post transcriptional landscapes required for the establishment of animal cell identities and functions. Overall design: Zebrafish embryos were dechorionated and injected at single cell stage with 1000pL of 75mM s4 UTP. Embryos were kept in the dark until collection time. Total RNA was extracted  and kept away from direct light   alkylated  used for library preparation with QuantSeq three prime mRNA Seq Library Prep Kit for Illumina FWD.", "parent bioproject:PRJNA1040928", null, null, "zebrafish 2hour wt 75mM s4u r1", "GSM7903256", null, "tissue:Embryos at 2 hpf of [AB TU]x[TL TLF]|geo loc name:missing|collection date:missing", "zebrafish 2hour wt 75mM s4u r1", "Slamdunk 0.4.3. Adapter sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC Reads that contain at least 2 T>C conversions were deemed labeled. Assembly: danRer11 Supplementary files format and content: Comma separated values  <.csv>; Total raw read and labeled read counts for all experiments and samples  including spike ins. Rows represent different three primeUTR isoforms for coding genes or full length transcript non coding genes. Columns represent: Ensembl gene IDs by itself non coding transcripts + three primeUTR isoforms coding transcripts  or ERCC IDs spike ins;  Chromosome name; Genomic start of feature; Genomic end of feature; DNA strand of feature; Number of Ts within feature;", "Embryos at 2 hpf", "Embryos were injected with 1000pL of 75mM s4 UTP.", "Trizol\u2122 QuantSeq 3\u2032 mRNA Seq Library Prep Kit for Illumina UDI Bundle FWD  Lexogen GmbH  cat. no. 144.96", "Zebrafish embryos were collected from natural breeding  with random mating parents  embryos were kept at 28.5 C in 0.5x Embryo Media.", "tissue:Embryos|Stage:2 hpf of [AB TU]x[TL TLF]", "GSM7903256", "GSM7903256: zebrafish 2hour wt 75mM s4u r1; Danio rerio; RNA Seq", "GSM7903256 r1", "GSM7903256", "1", "Trizol\u2122 QuantSeq 3\u2032 mRNA Seq Library Prep Kit for Illumina UDI Bundle FWD  Lexogen GmbH  cat. no. 144.96", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP472252", null, "loader:fastq load.py", "s2h_1.fastq.gz", "fastq", 4689849655.0, 46434155.0, "GSM7903256 r1", "0:101", "A:1611038201;C:846984275;G:953714532;T:1275424861;N:2687786", 101, null, null, null, 1611038201, 846984275, 953714532, 1275424861, 2687786, "SRX22541150", "SRS19550735", "SRA1751928", "Bazzini Lab, Stowers Institute for Medical Research", "Bazzini Lab, Stowers Institute for Medical Research", 1, 0.67301, null, 0.15612, null, 0.82171, null, 0.63462, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2023-11-15", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28937, "SRR26845671", "SRX22541149", "SRS19550733", "SRP472252", "PRJNA1040929", "Slam seq reveals that miR 430 regulates zygotic mRNA during zebrafish embryogenesis [timecourse data]", "GSE247933", "Other", "Background: Early embryonic developmental programs are guided by the coordinated interplay between maternally inherited and zygotically manufactured RNAs and proteins. Although these processes happen concomitantly and affecting gene function during this period is bound to affect both pools of mRNAs  it has been challenging to study their expression dynamics separately. Results: By employing Slam seq  a nascent mRNA labeling transcriptomic approach  in a developmental time series we observe that over half of the early zebrafish embryo transcriptome consists of maternal zygotic genes  emphasizing their pivotal role in early embryogenesis. We provide an hourly resolution of de novo transcriptional waves and follow nascent mRNA trajectories  finding that most de novo transcriptional events are stable throughout this period. Additionally  by blocking microRNA430 function  a key post transcriptional regulator during zebrafish embryogenesis  we directly show that it destabilizes hundreds of de novo transcribed mRNAs from pure zygotic as well as maternal zygotic genes. This unveils a novel miR 430 function during embryogenesis  fine tuning zygotic gene expression  which highlights that Slam seq can be used to disentangle transcriptional and post transcriptional regulation of mRNA levels.  Conclusion: Such valuable insights into zebrafish early embryo transcriptome dynamics emphasize the significance of post transcriptional regulators in zygotic genome activation. These findings pave the way for future investigations into the coordinated interplay between transcriptional and post transcriptional landscapes required for the establishment of animal cell identities and functions. Overall design: Zebrafish embryos were dechorionated and injected at single cell stage with 1000pL of 75mM s4 UTP. Embryos were kept in the dark until collection time. Total RNA was extracted  and kept away from direct light   alkylated  used for library preparation with QuantSeq three prime mRNA Seq Library Prep Kit for Illumina FWD.", "parent bioproject:PRJNA1040928", null, null, "zebrafish 1hour wt 75mM s4u r3", "GSM7903255", null, "tissue:Embryos at 1 hpf of [AB TU]x[TL TLF]|geo loc name:missing|collection date:missing", "zebrafish 1hour wt 75mM s4u r3", "Slamdunk 0.4.3. Adapter sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC Reads that contain at least 2 T>C conversions were deemed labeled. Assembly: danRer11 Supplementary files format and content: Comma separated values  <.csv>; Total raw read and labeled read counts for all experiments and samples  including spike ins. Rows represent different three primeUTR isoforms for coding genes or full length transcript non coding genes. Columns represent: Ensembl gene IDs by itself non coding transcripts + three primeUTR isoforms coding transcripts  or ERCC IDs spike ins;  Chromosome name; Genomic start of feature; Genomic end of feature; DNA strand of feature; Number of Ts within feature;", "Embryos at 1 hpf", "Embryos were injected with 1000pL of 75mM s4 UTP.", "Trizol\u2122 QuantSeq 3\u2032 mRNA Seq Library Prep Kit for Illumina UDI Bundle FWD  Lexogen GmbH  cat. no. 144.96", "Zebrafish embryos were collected from natural breeding  with random mating parents  embryos were kept at 28.5 C in 0.5x Embryo Media.", "tissue:Embryos|Stage:1 hpf of [AB TU]x[TL TLF]", "GSM7903255", "GSM7903255: zebrafish 1hour wt 75mM s4u r3; Danio rerio; RNA Seq", "GSM7903255 r1", "GSM7903255", "1", "Trizol\u2122 QuantSeq 3\u2032 mRNA Seq Library Prep Kit for Illumina UDI Bundle FWD  Lexogen GmbH  cat. no. 144.96", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP472252", null, "loader:fastq load.py", "s1h_3.fastq.gz", "fastq", 5540992108.0, 54861308.0, "GSM7903255 r1", "0:101", "A:1856189531;C:1011042624;G:1124613529;T:1546055477;N:3090947", 101, null, null, null, 1856189531, 1011042624, 1124613529, 1546055477, 3090947, "SRX22541149", "SRS19550733", "SRA1751928", "Bazzini Lab, Stowers Institute for Medical Research", "Bazzini Lab, Stowers Institute for Medical Research", 1, 0.72187, null, 0.16436, null, 0.82416, null, 0.64431, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2023-11-15", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28938, "SRR26845672", "SRX22541148", "SRS19550734", "SRP472252", "PRJNA1040929", "Slam seq reveals that miR 430 regulates zygotic mRNA during zebrafish embryogenesis [timecourse data]", "GSE247933", "Other", "Background: Early embryonic developmental programs are guided by the coordinated interplay between maternally inherited and zygotically manufactured RNAs and proteins. Although these processes happen concomitantly and affecting gene function during this period is bound to affect both pools of mRNAs  it has been challenging to study their expression dynamics separately. Results: By employing Slam seq  a nascent mRNA labeling transcriptomic approach  in a developmental time series we observe that over half of the early zebrafish embryo transcriptome consists of maternal zygotic genes  emphasizing their pivotal role in early embryogenesis. We provide an hourly resolution of de novo transcriptional waves and follow nascent mRNA trajectories  finding that most de novo transcriptional events are stable throughout this period. Additionally  by blocking microRNA430 function  a key post transcriptional regulator during zebrafish embryogenesis  we directly show that it destabilizes hundreds of de novo transcribed mRNAs from pure zygotic as well as maternal zygotic genes. This unveils a novel miR 430 function during embryogenesis  fine tuning zygotic gene expression  which highlights that Slam seq can be used to disentangle transcriptional and post transcriptional regulation of mRNA levels.  Conclusion: Such valuable insights into zebrafish early embryo transcriptome dynamics emphasize the significance of post transcriptional regulators in zygotic genome activation. These findings pave the way for future investigations into the coordinated interplay between transcriptional and post transcriptional landscapes required for the establishment of animal cell identities and functions. Overall design: Zebrafish embryos were dechorionated and injected at single cell stage with 1000pL of 75mM s4 UTP. Embryos were kept in the dark until collection time. Total RNA was extracted  and kept away from direct light   alkylated  used for library preparation with QuantSeq three prime mRNA Seq Library Prep Kit for Illumina FWD.", "parent bioproject:PRJNA1040928", null, null, "zebrafish 1hour wt 75mM s4u r2", "GSM7903254", null, "tissue:Embryos at 1 hpf of [AB TU]x[TL TLF]|geo loc name:missing|collection date:missing", "zebrafish 1hour wt 75mM s4u r2", "Slamdunk 0.4.3. Adapter sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC Reads that contain at least 2 T>C conversions were deemed labeled. Assembly: danRer11 Supplementary files format and content: Comma separated values  <.csv>; Total raw read and labeled read counts for all experiments and samples  including spike ins. Rows represent different three primeUTR isoforms for coding genes or full length transcript non coding genes. Columns represent: Ensembl gene IDs by itself non coding transcripts + three primeUTR isoforms coding transcripts  or ERCC IDs spike ins;  Chromosome name; Genomic start of feature; Genomic end of feature; DNA strand of feature; Number of Ts within feature;", "Embryos at 1 hpf", "Embryos were injected with 1000pL of 75mM s4 UTP.", "Trizol\u2122 QuantSeq 3\u2032 mRNA Seq Library Prep Kit for Illumina UDI Bundle FWD  Lexogen GmbH  cat. no. 144.96", "Zebrafish embryos were collected from natural breeding  with random mating parents  embryos were kept at 28.5 C in 0.5x Embryo Media.", "tissue:Embryos|Stage:1 hpf of [AB TU]x[TL TLF]", "GSM7903254", "GSM7903254: zebrafish 1hour wt 75mM s4u r2; Danio rerio; RNA Seq", "GSM7903254 r1", "GSM7903254", "1", "Trizol\u2122 QuantSeq 3\u2032 mRNA Seq Library Prep Kit for Illumina UDI Bundle FWD  Lexogen GmbH  cat. no. 144.96", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP472252", null, "loader:fastq load.py", "s1h_2.fastq.gz", "fastq", 4572239397.0, 45269697.0, "GSM7903254 r1", "0:101", "A:1530268631;C:831534079;G:915378596;T:1292534173;N:2523918", 101, null, null, null, 1530268631, 831534079, 915378596, 1292534173, 2523918, "SRX22541148", "SRS19550734", "SRA1751928", "Bazzini Lab, Stowers Institute for Medical Research", "Bazzini Lab, Stowers Institute for Medical Research", 1, 0.72394, null, 0.15187, null, 0.81753, null, 0.63236, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2023-11-15", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28939, "SRR26845673", "SRX22541147", "SRS19550732", "SRP472252", "PRJNA1040929", "Slam seq reveals that miR 430 regulates zygotic mRNA during zebrafish embryogenesis [timecourse data]", "GSE247933", "Other", "Background: Early embryonic developmental programs are guided by the coordinated interplay between maternally inherited and zygotically manufactured RNAs and proteins. Although these processes happen concomitantly and affecting gene function during this period is bound to affect both pools of mRNAs  it has been challenging to study their expression dynamics separately. Results: By employing Slam seq  a nascent mRNA labeling transcriptomic approach  in a developmental time series we observe that over half of the early zebrafish embryo transcriptome consists of maternal zygotic genes  emphasizing their pivotal role in early embryogenesis. We provide an hourly resolution of de novo transcriptional waves and follow nascent mRNA trajectories  finding that most de novo transcriptional events are stable throughout this period. Additionally  by blocking microRNA430 function  a key post transcriptional regulator during zebrafish embryogenesis  we directly show that it destabilizes hundreds of de novo transcribed mRNAs from pure zygotic as well as maternal zygotic genes. This unveils a novel miR 430 function during embryogenesis  fine tuning zygotic gene expression  which highlights that Slam seq can be used to disentangle transcriptional and post transcriptional regulation of mRNA levels.  Conclusion: Such valuable insights into zebrafish early embryo transcriptome dynamics emphasize the significance of post transcriptional regulators in zygotic genome activation. These findings pave the way for future investigations into the coordinated interplay between transcriptional and post transcriptional landscapes required for the establishment of animal cell identities and functions. Overall design: Zebrafish embryos were dechorionated and injected at single cell stage with 1000pL of 75mM s4 UTP. Embryos were kept in the dark until collection time. Total RNA was extracted  and kept away from direct light   alkylated  used for library preparation with QuantSeq three prime mRNA Seq Library Prep Kit for Illumina FWD.", "parent bioproject:PRJNA1040928", null, null, "zebrafish 1hour wt 75mM s4u r1", "GSM7903253", null, "tissue:Embryos at 1 hpf of [AB TU]x[TL TLF]|geo loc name:missing|collection date:missing", "zebrafish 1hour wt 75mM s4u r1", "Slamdunk 0.4.3. Adapter sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC Reads that contain at least 2 T>C conversions were deemed labeled. Assembly: danRer11 Supplementary files format and content: Comma separated values  <.csv>; Total raw read and labeled read counts for all experiments and samples  including spike ins. Rows represent different three primeUTR isoforms for coding genes or full length transcript non coding genes. Columns represent: Ensembl gene IDs by itself non coding transcripts + three primeUTR isoforms coding transcripts  or ERCC IDs spike ins;  Chromosome name; Genomic start of feature; Genomic end of feature; DNA strand of feature; Number of Ts within feature;", "Embryos at 1 hpf", "Embryos were injected with 1000pL of 75mM s4 UTP.", "Trizol\u2122 QuantSeq 3\u2032 mRNA Seq Library Prep Kit for Illumina UDI Bundle FWD  Lexogen GmbH  cat. no. 144.96", "Zebrafish embryos were collected from natural breeding  with random mating parents  embryos were kept at 28.5 C in 0.5x Embryo Media.", "tissue:Embryos|Stage:1 hpf of [AB TU]x[TL TLF]", "GSM7903253", "GSM7903253: zebrafish 1hour wt 75mM s4u r1; Danio rerio; RNA Seq", "GSM7903253 r1", "GSM7903253", "1", "Trizol\u2122 QuantSeq 3\u2032 mRNA Seq Library Prep Kit for Illumina UDI Bundle FWD  Lexogen GmbH  cat. no. 144.96", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP472252", null, "loader:fastq load.py", "s1h_1.fastq.gz", "fastq", 4271986597.0, 42296897.0, "GSM7903253 r1", "0:101", "A:1447221671;C:787487923;G:887526673;T:1147409594;N:2340736", 101, null, null, null, 1447221671, 787487923, 887526673, 1147409594, 2340736, "SRX22541147", "SRS19550732", "SRA1751928", "Bazzini Lab, Stowers Institute for Medical Research", "Bazzini Lab, Stowers Institute for Medical Research", 1, 0.68805, null, 0.18469, null, 0.83175, null, 0.62945, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2023-11-15", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [29229, "SRR27489746", "SRX23160963", "SRS20111121", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 2hpf replica C", "MPRA repC fractions 8 9 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:36|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 2hpf replica C", "Library 36", "Library 36", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 13085558528.0, 43329664.0, "BSSE QGF 206671 HGWLYDSX3 3 MPRA repC fractions 8 9 2hpf ATATGGAT CTGTATTA S36 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3305413622;C:3391845548;G:3249932870;T:3137708503;N:657985", 151, 151, null, null, 3305413622, 3391845548, 3249932870, 3137708503, 657985, "SRX23160963", "SRS20111121", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01098, 8e-05, 0.00025, 0.0, 0.99216, 0.99973, 0.4317, 0.61538, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29230, "SRR27489747", "SRX23160962", "SRS20111119", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 2hpf replica C", "MPRA repC fractions 6 7 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:35|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 2hpf replica C", "Library 35", "Library 35", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 16647721914.0, 55124907.0, "BSSE QGF 206670 HGWLYDSX3 3 MPRA repC fractions 6 7 2hpf CGGACAAC TCCGGATT S35 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4231542934;C:4348688006;G:4050131444;T:4016534422;N:825108", 151, 151, null, null, 4231542934, 4348688006, 4050131444, 4016534422, 825108, "SRX23160962", "SRS20111119", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01514, 0.00017, 0.00035, 3e-05, 0.99109, 0.99955, 0.4372, 0.30434, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29231, "SRR27489748", "SRX23160961", "SRS20111118", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 2hpf replica C", "MPRA repC fractions 4 5 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:34|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 2hpf replica C", "Library 34", "Library 34", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 15431181052.0, 51096626.0, "BSSE QGF 206669 HGWLYDSX3 3 MPRA repC fractions 4 5 2hpf TAAGTGGT CTTAAGCC S34 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3856018869;C:4036338306;G:3877988553;T:3660059325;N:775999", 151, 151, null, null, 3856018869, 4036338306, 3877988553, 3660059325, 775999, "SRX23160961", "SRS20111118", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01114, 8e-05, 0.00028, 0.0, 0.99192, 0.99975, 0.42956, 0.5, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29232, "SRR27489749", "SRX23160960", "SRS20111117", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 2hpf replica C", "MPRA repC input 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:33|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 2hpf replica C", "Library 33", "Library 33", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 11771229160.0, 38977580.0, "BSSE QGF 206668 HGWLYDSX3 3 MPRA repC input 2hpf CTACGACA GAGTCCAA S33 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2999574420;C:3115525474;G:2806539264;T:2849003922;N:586080", 151, 151, null, null, 2999574420, 3115525474, 2806539264, 2849003922, 586080, "SRX23160960", "SRS20111117", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01997, 2e-05, 0.00054, 0.0, 0.99022, 0.99993, 0.41853, 0.33333, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29235, "SRR27489752", "SRX23160957", "SRS20111114", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 2hpf replica A", "MPRA repA fractions 8 9 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:4|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 2hpf replica A", "Library 4", "Library 4", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 12108626278.0, 40094789.0, "BSSE QGF 206639 HGWLYDSX3 3 MPRA repA fractions 8 9 2hpf GCTTGTCA GAACATAC S4 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3079403604;C:3149095123;G:2953175005;T:2926352278;N:600268", 151, 151, null, null, 3079403604, 3149095123, 2953175005, 2926352278, 600268, "SRX23160957", "SRS20111114", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.014, 5e-05, 0.00032, 0.0, 0.99137, 0.99987, 0.45127, 0.28571, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29246, "SRR27489763", "SRX23160946", "SRS20111108", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 2hpf replica A", "MPRA repA fractions 6 7 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:3|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 2hpf replica A", "Library 3", "Library 3", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 12524202136.0, 41470868.0, "BSSE QGF 206638 HGWLYDSX3 3 MPRA repA fractions 6 7 2hpf ATCCACTG AGGTGCGT S3 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3168466372;C:3269998328;G:3075956662;T:3009160932;N:619842", 151, 151, null, null, 3168466372, 3269998328, 3075956662, 3009160932, 619842, "SRX23160946", "SRS20111108", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01351, 7e-05, 0.00028, 0.0, 0.99168, 0.99977, 0.43472, 0.54545, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29247, "SRR27489764", "SRX23160945", "SRS20111103", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 2hpf replica B", "MPRA repB fractions 8 9 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:20|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 2hpf replica B", "Library 20", "Library 20", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 12514444214.0, 41438557.0, "BSSE QGF 206655 HGWLYDSX3 3 MPRA repB fractions 8 9 2hpf AACGTTCC GGAGTACT S20 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3174354240;C:3246812350;G:3082021359;T:3010633962;N:622303", 151, 151, null, null, 3174354240, 3246812350, 3082021359, 3010633962, 622303, "SRX23160945", "SRS20111103", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01121, 0.00016, 0.00027, 1e-05, 0.99204, 0.99953, 0.43533, 0.5, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29248, "SRR27489765", "SRX23160944", "SRS20111102", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 2hpf replica B", "MPRA repB fractions 6 7 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:19|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 2hpf replica B", "Library 19", "Library 19", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 16535129670.0, 54752085.0, "BSSE QGF 206654 HGWLYDSX3 3 MPRA repB fractions 6 7 2hpf GGTACCTT AAGACGTC S19 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4184643114;C:4312135767;G:4051628900;T:3985895468;N:826421", 151, 151, null, null, 4184643114, 4312135767, 4051628900, 3985895468, 826421, "SRX23160944", "SRS20111102", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01416, 0.00017, 0.00031, 1e-05, 0.9917, 0.99941, 0.40732, 0.6, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29249, "SRR27489766", "SRX23160943", "SRS20111101", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 2hpf replica B", "MPRA repB fractions 4 5 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:18|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 2hpf replica B", "Library 18", "Library 18", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 12692870042.0, 42029371.0, "BSSE QGF 206653 HGWLYDSX3 3 MPRA repB fractions 4 5 2hpf GCACGGAC GTCTCGCA S18 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3179006274;C:3325152682;G:3173386021;T:3014687781;N:637284", 151, 151, null, null, 3179006274, 3325152682, 3173386021, 3014687781, 637284, "SRX23160943", "SRS20111101", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01199, 8e-05, 0.0003, 1e-05, 0.99145, 0.99979, 0.40897, 0.36363, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29250, "SRR27489767", "SRX23160942", "SRS20111100", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 2hpf replica B", "MPRA repB input 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:17|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 2hpf replica B", "Library 17", "Library 17", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 13169436008.0, 43607404.0, "BSSE QGF 206652 HGWLYDSX3 3 MPRA repB input 2hpf ATGTAAGT ACTCTATG S17 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3341908647;C:3485072739;G:3171200836;T:3170595031;N:658755", 151, 151, null, null, 3341908647, 3485072739, 3171200836, 3170595031, 658755, "SRX23160942", "SRS20111100", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01868, 5e-05, 0.0006, 0.0, 0.99038, 0.99983, 0.41955, 0.125, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29257, "SRR27489774", "SRX23160935", "SRS20111093", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 2hpf replica A", "MPRA repA fractions 4 5 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:2|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 2hpf replica A", "Library 2", "Library 2", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206637_HGWLYDSX3_3_MPRA_repA_fractions_4_5_2hpf_TTGGACTT_TATGAGTA_S2_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206637_HGWLYDSX3_3_MPRA_repA_fractions_4_5_2hpf_TTGGACTT_TATGAGTA_S2_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 16111078182.0, 53347941.0, "BSSE QGF 206637 HGWLYDSX3 3 MPRA repA fractions 4 5 2hpf TTGGACTT TATGAGTA S2 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4069536779;C:4222816450;G:3957789955;T:3860129964;N:805034", 151, 151, null, null, 4069536779, 4222816450, 3957789955, 3860129964, 805034, "SRX23160935", "SRS20111093", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01511, 5e-05, 0.00034, 0.0, 0.99135, 0.99985, 0.41564, 0.42857, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29258, "SRR27489775", "SRX23160934", "SRS20111092", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 2hpf replica A", "MPRA repA input 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:1|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 2hpf replica A", "Library 1", "Library 1", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206636_HGWLYDSX3_3_MPRA_repA_input_2hpf_GGACTTGG_CGCAGACG_S1_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206636_HGWLYDSX3_3_MPRA_repA_input_2hpf_GGACTTGG_CGCAGACG_S1_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 9769305890.0, 32348695.0, "BSSE QGF 206636 HGWLYDSX3 3 MPRA repA input 2hpf GGACTTGG CGCAGACG S1 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2477269774;C:2598109179;G:2338444856;T:2354997596;N:484485", 151, 151, null, null, 2477269774, 2598109179, 2338444856, 2354997596, 484485, "SRX23160934", "SRS20111092", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.0205, 4e-05, 0.00059, 0.0, 0.99013, 0.99987, 0.41957, 0.33333, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 676, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation\" = :p0 order by rowid limit 101", "params": {"p0": "Cleavage"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 480, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "OTHER", "label": "OTHER", "count": 166, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_strategy=OTHER", "selected": false}, {"value": "RIP-Seq", "label": "RIP-Seq", "count": 25, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_strategy=RIP-Seq", "selected": false}, {"value": "Bisulfite-Seq", "label": "Bisulfite-Seq", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_strategy=Bisulfite-Seq", "selected": false}, {"value": "FL-cDNA", "label": "FL-cDNA", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_strategy=FL-cDNA", "selected": false}, {"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_strategy=miRNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 674, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_source=TRANSCRIPTOMIC", "selected": false}, {"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage", "results": [{"value": "cDNA", "label": "cDNA", "count": 385, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=cDNA", "selected": false}, {"value": "unspecified", "label": "unspecified", "count": 133, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified", "selected": false}, {"value": "other", "label": "other", "count": 110, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=other", "selected": false}, {"value": "Oligo-dT", "label": "Oligo-dT", "count": 21, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=Oligo-dT", "selected": false}, {"value": "RT-PCR", "label": "RT-PCR", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=RT-PCR", "selected": false}, {"value": "size fractionation", "label": "size fractionation", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=size+fractionation", "selected": false}, {"value": "RANDOM", "label": "RANDOM", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=RANDOM", "selected": false}, {"value": "CAGE", "label": "CAGE", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=CAGE", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 445, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_layout=SINGLE", "selected": false}, {"value": "PAIRED", "label": "PAIRED", "count": 231, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 660, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.platform=ILLUMINA", "selected": false}, {"value": "ION_TORRENT", "label": "ION_TORRENT", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.platform=ION_TORRENT", "selected": false}, {"value": "ABI_SOLID", "label": "ABI_SOLID", "count": 5, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.platform=ABI_SOLID", "selected": false}, {"value": "PACBIO_SMRT", "label": "PACBIO_SMRT", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.platform=PACBIO_SMRT", "selected": false}, {"value": "OXFORD_NANOPORE", "label": "OXFORD_NANOPORE", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.platform=OXFORD_NANOPORE", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage", "results": [{"value": "Embryo", "label": "Embryo", "count": 676, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage", "results": [{"value": "Cleavage", "label": "Cleavage", "count": 676, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 651, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&tissue_curation_coarse=All+anatomical+structures", "selected": false}, {"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 20, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&tissue_curation_coarse=Embryo+Imprecise", "selected": false}, {"value": "Cardiovascular System", "label": "Cardiovascular System", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&tissue_curation_coarse=Cardiovascular+System", "selected": false}, {"value": "Reproductive System", "label": "Reproductive System", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&tissue_curation_coarse=Reproductive+System", "selected": false}, {"value": "Surface Structure", "label": "Surface Structure", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&tissue_curation_coarse=Surface+Structure", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage", "results": [{"value": "Whole Organism", "label": "Whole Organism", "count": 364, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&tissue_curation=Whole+Organism", "selected": false}, {"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 287, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&tissue_curation=Embryo+Imprecise", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 20, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&tissue_curation=Undetermined", "selected": false}, {"value": "Heart", "label": "Heart", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&tissue_curation=Heart", "selected": false}, {"value": "Oocyte", "label": "Oocyte", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&tissue_curation=Oocyte", "selected": false}, {"value": "Trunk", "label": "Trunk", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&tissue_curation=Trunk", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage", "results": [{"value": "unknown", "label": "unknown", "count": 613, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&technology=unknown", "selected": false}, {"value": "bulk", "label": "bulk", "count": 39, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&technology=bulk", "selected": false}, {"value": "iclip", "label": "iclip", "count": 20, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&technology=iclip", "selected": false}, {"value": "10x", "label": "10x", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&technology=10x", "selected": false}, {"value": "generic-scrnaseq-only", "label": "generic-scrnaseq-only", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&technology=generic-scrnaseq-only", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": "29258", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&_next=29258", "private": false, "allow_execute_sql": true, "query_ms": 101.08564399706665}