{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"unspecified\", experiment.library_strategy = \"OTHER\" and tissue_curation = \"Embryo Imprecise\"", "rows": [[43058, "SRR8354695", "SRX5165478", "SRS4174524", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. 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However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS seq RNA structure positive controls in vitro replicate 1;DMS seq RNA structure positive controls in vitro replicate 2", "Raw multiplex: DMS seq RNA positives ctrl in vitro B1 AG01489;DMS seq RNA positives ctrl in vitro B2 AG01490", null, "strain:TU/AB|age:3.7|dev stage:oblong|sex:pooled male and female|tissue:embryo|treatment:0.5% DMS for 10 min in vitro|molecule:RNA|condition:invitro DMS|replicate group:1|replicate:1;2|barcode:TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS seq RNA structure positive controls in vitro replicate 1;DMS seq RNA structure positive controls in vitro replicate 2", "AG01489.1;AG01490.1", "AG01489.1;AG01490.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MYYANXX_JBDX127_009_R1.fastq.gz", "fastq", 1115150128.0, 14673028.0, "C7MYYANXX JBDX127 009 R1.fastq.gz", "0:76", "A:313482382;C:276309346;G:291633361;T:233659719;N:65320", 76, null, null, null, 313482382, 276309346, 291633361, 233659719, 65320, "SRX5165476", "SRS4174522", "SRA825010", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00546, null, 0.00047, null, 0.98602, null, 0.51535, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-12-19", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43061, "SRR7264565", "SRX4168732", "SRS3380685", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. 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These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated", "Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated", null, "strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated", "AG01046.1;AG01047.1;AG01049.1;unrelated", "AG01046.1;AG01047.1;AG01049.1;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA1YWADXX_JBBS71_021_R1.fastq.gz", "fastq", 1444702012.0, 19009237.0, "HA1YWADXX JBBS71 021 R1.fastq.gz", "0:76", "A:442549747;C:365473385;G:344546726;T:292070542;N:61612", 76, null, null, null, 442549747, 365473385, 344546726, 292070542, 61612, "SRX4168731", "SRS3380685", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43063, "SRR7264567", "SRX4168730", "SRS3380690", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. 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These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated", "Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated", null, "strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated", "AG01042.6;AG01043.6;AG01044.6;unrelated", "AG01042.6;AG01043.6;AG01044.6;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HBCAFADXX_JBBR70_020_R1.fastq.gz", "fastq", 3562176468.0, 46870743.0, "HBCAFADXX JBBR70 020 R1.fastq.gz", "0:76", "A:1097921080;C:906895047;G:849908073;T:707369464;N:82804", 76, null, null, null, 1097921080, 906895047, 849908073, 707369464, 82804, "SRX4168730", "SRS3380690", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43064, "SRR7264568", "SRX4168729", "SRS3380690", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated", "Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated", null, "strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated", "AG01042.5;AG01043.5;AG01044.5;unrelated", "AG01042.5;AG01043.5;AG01044.5;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "C562AACXX_JBBR70_NOBCX_R1.fastq.gz", "fastq", 13352386192.0, 175689292.0, "C562AACXX JBBR70 NOBCX R1.fastq.gz", "0:76", "A:4126007145;C:3372127203;G:3172182791;T:2661287884;N:20781169", 76, null, null, null, 4126007145, 3372127203, 3172182791, 2661287884, 20781169, "SRX4168729", "SRS3380690", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43065, "SRR7264569", "SRX4168728", "SRS3380690", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. 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However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated", "Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated", null, "strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated", "AG01042.3;AG01043.3;AG01044.3;unrelated", "AG01042.3;AG01043.3;AG01044.3;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA1YVADXX_JBBR70_NOBCX_R1.fastq.gz", "fastq", 7892000132.0, 103842107.0, "HA1YVADXX JBBR70 NOBCX R1.fastq.gz", "0:76", "A:2428266964;C:2007082407;G:1885147455;T:1568726692;N:2776614", 76, null, null, null, 2428266964, 2007082407, 1885147455, 1568726692, 2776614, "SRX4168727", "SRS3380690", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43067, "SRR7264571", "SRX4168726", "SRS3380690", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated", "Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated", null, "strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated", "AG01042.2;AG01043.2;AG01044.2;unrelated", "AG01042.2;AG01043.2;AG01044.2;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA22NADXX_JBBR70_020_R1.fastq.gz", "fastq", 554569568.0, 7296968.0, "HA22NADXX JBBR70 020 R1.fastq.gz", "0:76", "A:168630291;C:138451887;G:131779810;T:108186590;N:7520990", 76, null, null, null, 168630291, 138451887, 131779810, 108186590, 7520990, "SRX4168726", "SRS3380690", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43068, "SRR7264572", "SRX4168725", "SRS3380690", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated", "Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated", null, "strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT sphere in vivo;DMS Seq WT shield in vivo;unrelated", "AG01042.1;AG01043.1;AG01044.1;unrelated", "AG01042.1;AG01043.1;AG01044.1;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA1YWADXX_JBBR70_020_R1.fastq.gz", "fastq", 1565371316.0, 20596991.0, "HA1YWADXX JBBR70 020 R1.fastq.gz", "0:76", "A:481887814;C:398331513;G:374271346;T:310815367;N:65276", 76, null, null, null, 481887814, 398331513, 374271346, 310815367, 65276, "SRX4168725", "SRS3380690", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43069, "SRR7264573", "SRX4168724", "SRS3380685", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated", "Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated", null, "strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated", "AG01046.4;AG01047.4;AG01049.4;unrelated", "AG01046.4;AG01047.4;AG01049.4;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA2H1ADXX_JBBS71_NOBCX_R1.fastq.gz", "fastq", 8845878184.0, 116393134.0, "HA2H1ADXX JBBS71 NOBCX R1.fastq.gz", "0:76", "A:2711637569;C:2235324807;G:2105535243;T:1791610098;N:1770467", 76, null, null, null, 2711637569, 2235324807, 2105535243, 1791610098, 1770467, "SRX4168724", "SRS3380685", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43070, "SRR7264574", "SRX4168723", "SRS3380685", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated", "Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated", null, "strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated", "AG01046.3;AG01047.3;AG01049.3;unrelated", "AG01046.3;AG01047.3;AG01049.3;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA1YVADXX_JBBS71_NOBCX_R1.fastq.gz", "fastq", 7768733452.0, 102220177.0, "HA1YVADXX JBBS71 NOBCX R1.fastq.gz", "0:76", "A:2378019627;C:1963788516;G:1851111018;T:1572409542;N:3404749", 76, null, null, null, 2378019627, 1963788516, 1851111018, 1572409542, 3404749, "SRX4168723", "SRS3380685", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 1e-05, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43071, "SRR7264575", "SRX4168722", "SRS3380686", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2", "Raw multiplex: dmsseq AG01273;dmsseq AG01274", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2", "AG01273.4;AG01274.4", "AG01273.4;AG01274.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HWKVWADXX_JBCZ103_023_R1.fastq.gz", "fastq", 7514617040.0, 98876540.0, "HWKVWADXX JBCZ103 023 R1.fastq.gz", "0:76", "A:2401597632;C:1861527917;G:1834777254;T:1415956870;N:757367", 76, null, null, null, 2401597632, 1861527917, 1834777254, 1415956870, 757367, "SRX4168722", "SRS3380686", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43072, "SRR7264576", "SRX4168721", "SRS3380689", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: RPF patA WT 64c RPF B1;RPF patA WT 64c RPF B2", "Raw multiplex: ribo seq pata AG01409;ribo seq pata AG01410", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:cyclohex|molecule:RNA|condition:RPF 28nt|replicate group:19|replicate:1;2|barcode:CACA;TCTC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: RPF patA WT 64c RPF B1;RPF patA WT 64c RPF B2", "AG01409.1;AG01410.1", "AG01409.1;AG01410.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MPPANXX_JBDL115_014_R1.fastq.gz", "fastq", 4944760108.0, 65062633.0, "C7MPPANXX JBDL115 014 R1.fastq.gz", "0:76", "A:1280812305;C:1385761238;G:1441128504;T:836702863;N:355198", 76, null, null, null, 1280812305, 1385761238, 1441128504, 836702863, 355198, "SRX4168721", "SRS3380689", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43073, "SRR7264577", "SRX4168720", "SRS3380688", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: RPF patA WT 64c PatA RPF B1;RPF patA WT 64c PatA RPF B2", "Raw multiplex: ribo seq pata AG01411;ribo seq pata AG01412", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:cyclohex PatA|molecule:RNA|condition:RPF 28nt|replicate group:20|replicate:1;2|barcode:CACA;TCTC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: RPF patA WT 64c PatA RPF B1;RPF patA WT 64c PatA RPF B2", "AG01411.1;AG01412.1", "AG01411.1;AG01412.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MPPANXX_JBDM116_015_R1.fastq.gz", "fastq", 10995071544.0, 144671994.0, "C7MPPANXX JBDM116 015 R1.fastq.gz", "0:76", "A:2850888928;C:3075001734;G:3215965099;T:1852417694;N:798089", 76, null, null, null, 2850888928, 3075001734, 3215965099, 1852417694, 798089, "SRX4168720", "SRS3380688", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43074, "SRR7264578", "SRX4168719", "SRS3380687", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2", "Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2", "AG01426.1;AG01427.1", "AG01426.1;AG01427.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MPPANXX_JBDF109_027_R1.fastq.gz", "fastq", 446991948.0, 5881473.0, "C7MPPANXX JBDF109 027 R1.fastq.gz", "0:76", "A:146192524;C:109441919;G:103882304;T:87445288;N:29913", 76, null, null, null, 146192524, 109441919, 103882304, 87445288, 29913, "SRX4168719", "SRS3380687", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 2e-05, null, 1e-05, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43075, "SRR7264579", "SRX4168718", "SRS3380687", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2", "Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2", "AG01426.2;AG01427.2", "AG01426.2;AG01427.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJC2ADXX_JBDF109_027_R1.fastq.gz", "fastq", 447485492.0, 5887967.0, "HVJC2ADXX JBDF109 027 R1.fastq.gz", "0:76", "A:146683880;C:109166579;G:104154702;T:87473352;N:6979", 76, null, null, null, 146683880, 109166579, 104154702, 87473352, 6979, "SRX4168718", "SRS3380687", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0023, null, 0.00034, null, 0.99326, null, 0.57567, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43076, "SRR7264580", "SRX4168717", "SRS3380687", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2", "Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2", "AG01426.3;AG01427.3", "AG01426.3;AG01427.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJ2TADXX_JBDF109_027_R1.fastq.gz", "fastq", 4740289176.0, 62372226.0, "HVJ2TADXX JBDF109 027 R1.fastq.gz", "0:76", "A:1552060471;C:1156267615;G:1104246757;T:927209997;N:504336", 76, null, null, null, 1552060471, 1156267615, 1104246757, 927209997, 504336, "SRX4168717", "SRS3380687", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00235, null, 0.00026, null, 0.99379, null, 0.60051, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43077, "SRR7264581", "SRX4168716", "SRS3380687", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2", "Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2", "AG01426.4;AG01427.4", "AG01426.4;AG01427.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HJTYNBCXX_JBDF109_NOBCX_R1.fastq.gz", "fastq", 6776423036.0, 89163461.0, "HJTYNBCXX JBDF109 NOBCX R1.fastq.gz", "0:76", "A:2212424663;C:1653496002;G:1573846163;T:1336100302;N:555906", 76, null, null, null, 2212424663, 1653496002, 1573846163, 1336100302, 555906, "SRX4168716", "SRS3380687", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 3e-05, null, 2e-05, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43078, "SRR7264582", "SRX4168715", "SRS3380683", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2", "Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2", "AG01428.1;AG01429.1", "AG01428.1;AG01429.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MPPANXX_JBDG110_013_R1.fastq.gz", "fastq", 1593732388.0, 20970163.0, "C7MPPANXX JBDG110 013 R1.fastq.gz", "0:76", "A:517196379;C:393268952;G:372639155;T:310521534;N:106368", 76, null, null, null, 517196379, 393268952, 372639155, 310521534, 106368, "SRX4168715", "SRS3380683", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 2e-05, null, 0.0, null, 0.99997, null, 1.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43079, "SRR7264583", "SRX4168714", "SRS3380683", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2", "Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2", "AG01428.2;AG01429.2", "AG01428.2;AG01429.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJC2ADXX_JBDG110_013_R1.fastq.gz", "fastq", 1268326988.0, 16688513.0, "HVJC2ADXX JBDG110 013 R1.fastq.gz", "0:76", "A:411772190;C:312434121;G:297408612;T:246654231;N:57834", 76, null, null, null, 411772190, 312434121, 297408612, 246654231, 57834, "SRX4168714", "SRS3380683", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 1e-05, null, 0.0, null, 0.99997, null, 0.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43080, "SRR7264584", "SRX4168713", "SRS3380683", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2", "Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2", "AG01428.3;AG01429.3", "AG01428.3;AG01429.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJ2TADXX_JBDG110_013_R1.fastq.gz", "fastq", 1149592188.0, 15126213.0, "HVJ2TADXX JBDG110 013 R1.fastq.gz", "0:76", "A:373090462;C:283151050;G:269811169;T:223419849;N:119658", 76, null, null, null, 373090462, 283151050, 269811169, 223419849, 119658, "SRX4168713", "SRS3380683", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00222, null, 0.0002, null, 0.99362, null, 0.55643, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43081, "SRR7264585", "SRX4168712", "SRS3380686", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2", "Raw multiplex: dmsseq AG01273;dmsseq AG01274", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2", "AG01273.3;AG01274.3", "AG01273.3;AG01274.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJ7NADXX_JBCZ103_023_R1.fastq.gz", "fastq", 882016024.0, 11605474.0, "HVJ7NADXX JBCZ103 023 R1.fastq.gz", "0:76", "A:278837606;C:213606139;G:214029888;T:175477675;N:64716", 76, null, null, null, 278837606, 213606139, 214029888, 175477675, 64716, "SRX4168712", "SRS3380686", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 6e-05, null, 4e-05, null, 0.99995, null, 1.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43082, "SRR7264586", "SRX4168711", "SRS3380686", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2", "Raw multiplex: dmsseq AG01273;dmsseq AG01274", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2", "AG01273.2;AG01274.2", "AG01273.2;AG01274.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVK53ADXX_JBCZ103_023_R1.fastq.gz", "fastq", 2614864056.0, 34406106.0, "HVK53ADXX JBCZ103 023 R1.fastq.gz", "0:76", "A:832670351;C:647746556;G:639758530;T:494461931;N:226688", 76, null, null, null, 832670351, 647746556, 639758530, 494461931, 226688, "SRX4168711", "SRS3380686", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 5e-05, null, 2e-05, null, 0.99993, null, 0.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43083, "SRR7264587", "SRX4168710", "SRS3380684", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1", "AG01269.4;AG01270.4", "AG01269.4;AG01270.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MYYANXX_JBCX101_016_R1.fastq.gz", "fastq", 3504515800.0, 46112050.0, "C7MYYANXX JBCX101 016 R1.fastq.gz", "0:76", "A:1100987855;C:897481291;G:850509260;T:655386223;N:151171", 76, null, null, null, 1100987855, 897481291, 850509260, 655386223, 151171, "SRX4168710", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00251, null, 0.00024, null, 0.99334, null, 0.49363, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43084, "SRR7264588", "SRX4168709", "SRS3380684", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1", "AG01269.3;AG01270.3", "AG01269.3;AG01270.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJ7NADXX_JBCX101_016_R1.fastq.gz", "fastq", 1533760484.0, 20181059.0, "HVJ7NADXX JBCX101 016 R1.fastq.gz", "0:76", "A:486730101;C:387546602;G:372319444;T:287072948;N:91389", 76, null, null, null, 486730101, 387546602, 372319444, 287072948, 91389, "SRX4168709", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 4e-05, null, 2e-05, null, 0.99997, null, 1.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43085, "SRR7264589", "SRX4168708", "SRS3380686", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2", "Raw multiplex: dmsseq AG01273;dmsseq AG01274", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2", "AG01273.1;AG01274.1", "AG01273.1;AG01274.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HMHGVADXX_JBCZ103_023_R1.fastq.gz", "fastq", 2819768568.0, 37102218.0, "HMHGVADXX JBCZ103 023 R1.fastq.gz", "0:76", "A:900945260;C:699348182;G:689446355;T:529699985;N:328786", 76, null, null, null, 900945260, 699348182, 689446355, 529699985, 328786, "SRX4168708", "SRS3380686", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43086, "SRR7264590", "SRX4168707", "SRS3380684", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1", "AG01269.5;AG01270.5", "AG01269.5;AG01270.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MWLANXX_JBCX101_016_R1.fastq.gz", "fastq", 11187105076.0, 147198751.0, "C7MWLANXX JBCX101 016 R1.fastq.gz", "0:76", "A:3525623658;C:2869684594;G:2708534500;T:2083102664;N:159660", 76, null, null, null, 3525623658, 2869684594, 2708534500, 2083102664, 159660, "SRX4168707", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43087, "SRR7264591", "SRX4168706", "SRS3380685", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated", "Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated", null, "strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated", "AG01046.6;AG01047.6;AG01049.6;unrelated", "AG01046.6;AG01047.6;AG01049.6;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HBCAFADXX_JBBS71_021_R1.fastq.gz", "fastq", 5103002976.0, 67144776.0, "HBCAFADXX JBBS71 021 R1.fastq.gz", "0:76", "A:1565087315;C:1292145008;G:1214936605;T:1030712352;N:121696", 76, null, null, null, 1565087315, 1292145008, 1214936605, 1030712352, 121696, "SRX4168706", "SRS3380685", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 2e-05, null, 1e-05, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43088, "SRR7264592", "SRX4168705", "SRS3380685", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated", "Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated", null, "strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq WT 64c in vivo;DMS Seq WT shield in vivo;DMS Seq WT sphere in vivo;unrelated", "AG01046.5;AG01047.5;AG01049.5;unrelated", "AG01046.5;AG01047.5;AG01049.5;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "C562AACXX_JBBS71_NOBCX_R1.fastq.gz", "fastq", 11245730944.0, 147970144.0, "C562AACXX JBBS71 NOBCX R1.fastq.gz", "0:76", "A:3451642355;C:2826476753;G:2670179644;T:2277897894;N:19534298", 76, null, null, null, 3451642355, 2826476753, 2670179644, 2277897894, 19534298, "SRX4168705", "SRS3380685", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43089, "SRR7264593", "SRX4168704", "SRS3380684", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1", "AG01269.2;AG01270.2", "AG01269.2;AG01270.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVK53ADXX_JBCX101_016_R1.fastq.gz", "fastq", 4318423208.0, 56821358.0, "HVK53ADXX JBCX101 016 R1.fastq.gz", "0:76", "A:1370691469;C:1101595011;G:1048719303;T:796936406;N:481019", 76, null, null, null, 1370691469, 1101595011, 1048719303, 796936406, 481019, "SRX4168704", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 1e-05, null, 0.0, null, 0.99997, null, 0.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43090, "SRR7264594", "SRX4168703", "SRS3380684", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1", "AG01269.1;AG01270.1", "AG01269.1;AG01270.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HMHGVADXX_JBCX101_016_R1.fastq.gz", "fastq", 3247405520.0, 42729020.0, "HMHGVADXX JBCX101 016 R1.fastq.gz", "0:76", "A:1030573532;C:829398246;G:789085434;T:598013908;N:334400", 76, null, null, null, 1030573532, 829398246, 789085434, 598013908, 334400, "SRX4168703", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43091, "SRR7264595", "SRX4168702", "SRS3380683", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2", "Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2", "AG01428.5;AG01429.5", "AG01428.5;AG01429.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HJTYNBCXX_JBDG110_NOBCX_R1.fastq.gz", "fastq", 8473348224.0, 111491424.0, "HJTYNBCXX JBDG110 NOBCX R1.fastq.gz", "0:76", "A:2738474380;C:2086110939;G:1986494866;T:1661471870;N:796169", 76, null, null, null, 2738474380, 2086110939, 1986494866, 1661471870, 796169, "SRX4168702", "SRS3380683", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 3e-05, null, 2e-05, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43092, "SRR7264596", "SRX4168701", "SRS3380683", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2", "Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2", "AG01428.4;AG01429.4", "AG01428.4;AG01429.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJ7NADXX_JBDG110_013_R1.fastq.gz", "fastq", 1317100672.0, 17330272.0, "HVJ7NADXX JBDG110 013 R1.fastq.gz", "0:76", "A:424319849;C:318879376;G:308835829;T:264971153;N:94465", 76, null, null, null, 424319849, 318879376, 308835829, 264971153, 94465, "SRX4168701", "SRS3380683", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 9e-05, null, 5e-05, null, 0.99995, null, 0.2, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43093, "SRR5893052", "SRX3058793", "SRS2404523", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA 6h a Am pA RNA B1", "miniresa AG01714", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|replicate group:27|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA 6h a Am pA RNA B1", "AG01714.1", "AG01714.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01714.1_R1.fastq.gz", "fastq", 263900576.0, 3472376.0, "AG01714.1 R1.fastq.gz", "0:76", "A:71973779;C:48927629;G:51913512;T:91079622;N:6034", 76, null, null, null, 71973779, 48927629, 51913512, 91079622, 6034, "SRX3058793", "SRS2404523", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.9163, null, 3e-05, null, 0.99833, null, 0.61085, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43094, "SRR5893053", "SRX3058792", "SRS2404525", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA 6h a Am pA RNA B2", "miniresa AG01715", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|replicate group:27|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA 6h a Am pA RNA B2", "AG01715.1", "AG01715.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01715.1_R1.fastq.gz", "fastq", 233910976.0, 3077776.0, "AG01715.1 R1.fastq.gz", "0:76", "A:63827548;C:43163354;G:46127646;T:80731865;N:60563", 76, null, null, null, 63827548, 43163354, 46127646, 80731865, 60563, "SRX3058792", "SRS2404525", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.92571, null, 3e-05, null, 0.99809, null, 0.62106, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43095, "SRR5893054", "SRX3058791", "SRS2404524", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA 2h pA RNA B1", "miniresa AG01710", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:25|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA 2h pA RNA B1", "AG01710.1", "AG01710.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01710.1_R1.fastq.gz", "fastq", 236178588.0, 3107613.0, "AG01710.1 R1.fastq.gz", "0:76", "A:63902747;C:43772893;G:46507615;T:81990822;N:4511", 76, null, null, null, 63902747, 43772893, 46507615, 81990822, 4511, "SRX3058791", "SRS2404524", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.92111, null, 4e-05, null, 0.99799, null, 0.56316, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43096, "SRR5893055", "SRX3058790", "SRS2404526", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA 2h pA RNA B2", "miniresa AG01711", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:25|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA 2h pA RNA B2", "AG01711.1", "AG01711.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01711.1_R1.fastq.gz", "fastq", 226089360.0, 2974860.0, "AG01711.1 R1.fastq.gz", "0:76", "A:61341697;C:41846683;G:44622362;T:78273216;N:5402", 76, null, null, null, 61341697, 41846683, 44622362, 78273216, 5402, "SRX3058790", "SRS2404526", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.91845, null, 1e-05, null, 0.99797, null, 0.60522, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43097, "SRR5893056", "SRX3058789", "SRS2404529", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA 6h pA RNA B1", "miniresa AG01712", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:26|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA 6h pA RNA B1", "AG01712.1", "AG01712.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01712.1_R1.fastq.gz", "fastq", 247808716.0, 3260641.0, "AG01712.1 R1.fastq.gz", "0:76", "A:67604374;C:45731516;G:48975112;T:85491937;N:5777", 76, null, null, null, 67604374, 45731516, 48975112, 85491937, 5777, "SRX3058789", "SRS2404529", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.91668, null, 4e-05, null, 0.99837, null, 0.57941, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43098, "SRR5893057", "SRX3058788", "SRS2404527", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA 6h pA RNA B2", "miniresa AG01713", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:26|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA 6h pA RNA B2", "AG01713.1", "AG01713.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01713.1_R1.fastq.gz", "fastq", 314337748.0, 4136023.0, "AG01713.1 R1.fastq.gz", "0:76", "A:86391705;C:58569607;G:62248447;T:107120293;N:7696", 76, null, null, null, 86391705, 58569607, 62248447, 107120293, 7696, "SRX3058788", "SRS2404527", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.88475, null, 1e-05, null, 0.99845, null, 0.62559, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43103, "SRR5893062", "SRX3058783", "SRS2404532", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT 64c DMScontrol in vitro", "dmsseq AG00876", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:water in vitro|molecule:RNA|selection:pA|condition:control|replicate group:13|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c DMScontrol in vitro", "AG00876.2", "AG00876.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG00876.2_R1.fastq.gz", "fastq", 139395856.0, 1834156.0, "AG00876.2 R1.fastq.gz", "0:76", "A:37323535;C:39047425;G:34144869;T:28873865;N:6162", 76, null, null, null, 37323535, 39047425, 34144869, 28873865, 6162, "SRX3058783", "SRS2404532", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00316, null, 0.00094, null, 0.99318, null, 0.54676, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43104, "SRR5893063", "SRX3058782", "SRS2404532", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT 64c DMScontrol in vitro", "dmsseq AG00876", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:water in vitro|molecule:RNA|selection:pA|condition:control|replicate group:13|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c DMScontrol in vitro", "AG00876.1", "AG00876.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG00876.1_R1.fastq.gz", "fastq", 23244372.0, 305847.0, "AG00876.1 R1.fastq.gz", "0:76", "A:6246268;C:6429695;G:5629550;T:4937550;N:1309", 76, null, null, null, 6246268, 6429695, 5629550, 4937550, 1309, "SRX3058782", "SRS2404532", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.02737, null, 0.00562, null, 0.96288, null, 0.52983, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43105, "SRR5893072", "SRX3058773", "SRS2404537", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT shield in vivo", "dmsseq AG01044", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT shield in vivo", "AG01044.6", "AG01044.6", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01044.6_R1.fastq.gz", "fastq", 352399237.0, 15002980.0, "AG01044.6 R1.fastq.gz", "0:23.49 1:0", "A:95827007;C:78301278;G:87345623;T:90923434;N:1895", 23, 0, null, null, 95827007, 78301278, 87345623, 90923434, 1895, "SRX3058773", "SRS2404537", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.57991, null, 0.14096, null, 0.78833, null, 0.59313, null, 19, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43106, "SRR5893073", "SRX3058772", "SRS2404537", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT shield in vivo", "dmsseq AG01044", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT shield in vivo", "AG01044.5", "AG01044.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01044.5_R1.fastq.gz", "fastq", 1345288777.0, 56803082.0, "AG01044.5 R1.fastq.gz", "0:23.68 1:0", "A:365900523;C:297605434;G:332516082;T:349160736;N:106002", 23, 0, null, null, 365900523, 297605434, 332516082, 349160736, 106002, "SRX3058772", "SRS2404537", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.58577, null, 0.1419, null, 0.7875, null, 0.55349, null, 34, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43107, "SRR5893074", "SRX3058771", "SRS2404537", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT shield in vivo", "dmsseq AG01044", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT shield in vivo", "AG01044.4", "AG01044.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01044.4_R1.fastq.gz", "fastq", 914428539.0, 38790299.0, "AG01044.4 R1.fastq.gz", "0:23.57 1:0", "A:247816262;C:203789970;G:226994244;T:235814929;N:13134", 23, 0, null, null, 247816262, 203789970, 226994244, 235814929, 13134, "SRX3058771", "SRS2404537", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.58479, null, 0.14134, null, 0.7895, null, 0.58758, null, 17, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43108, "SRR5893075", "SRX3058770", "SRS2404537", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT shield in vivo", "dmsseq AG01044", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT shield in vivo", "AG01044.3", "AG01044.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01044.3_R1.fastq.gz", "fastq", 788379216.0, 33454094.0, "AG01044.3 R1.fastq.gz", "0:23.57 1:0", "A:213097014;C:176081523;G:196161554;T:203036893;N:2232", 23, 0, null, null, 213097014, 176081523, 196161554, 203036893, 2232, "SRX3058770", "SRS2404537", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.58292, null, 0.13842, null, 0.78975, null, 0.59022, null, 16, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43109, "SRR5893076", "SRX3058769", "SRS2404537", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT shield in vivo", "dmsseq AG01044", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT shield in vivo", "AG01044.2", "AG01044.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01044.2_R1.fastq.gz", "fastq", 53616540.0, 2286483.0, "AG01044.2 R1.fastq.gz", "0:23.45 1:0", "A:14492308;C:11955609;G:13424134;T:13741847;N:2642", 23, 0, null, null, 14492308, 11955609, 13424134, 13741847, 2642, "SRX3058769", "SRS2404537", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.56568, null, 0.13601, null, 0.79101, null, 0.59727, null, 26, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43110, "SRR5893077", "SRX3058768", "SRS2404537", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT shield in vivo", "dmsseq AG01044", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT shield in vivo", "AG01044.1", "AG01044.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01044.1_R1.fastq.gz", "fastq", 157041129.0, 6654774.0, "AG01044.1 R1.fastq.gz", "0:23.60 1:0", "A:42428242;C:35110921;G:39122952;T:40378347;N:667", 23, 0, null, null, 42428242, 35110921, 39122952, 40378347, 667, "SRX3058768", "SRS2404537", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.58493, null, 0.13991, null, 0.78735, null, 0.59014, null, 15, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43111, "SRR5893078", "SRX3058767", "SRS2404538", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT sphere in vivo", "dmsseq AG01043", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT sphere in vivo", "AG01043.6", "AG01043.6", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01043.6_R1.fastq.gz", "fastq", 245591088.0, 10387582.0, "AG01043.6 R1.fastq.gz", "0:23.64 1:0", "A:66848740;C:56927652;G:60996703;T:60816631;N:1362", 23, 0, null, null, 66848740, 56927652, 60996703, 60816631, 1362, "SRX3058767", "SRS2404538", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.62265, null, 0.12438, null, 0.7696, null, 0.59474, null, 32, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43112, "SRR5893079", "SRX3058766", "SRS2404538", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT sphere in vivo", "dmsseq AG01043", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT sphere in vivo", "AG01043.5", "AG01043.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01043.5_R1.fastq.gz", "fastq", 935516222.0, 39234795.0, "AG01043.5 R1.fastq.gz", "0:23.84 1:0", "A:254864411;C:216185186;G:231676738;T:232716892;N:72995", 23, 0, null, null, 254864411, 216185186, 231676738, 232716892, 72995, "SRX3058766", "SRS2404538", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.6326, null, 0.12713, null, 0.76739, null, 0.59812, null, 27, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43113, "SRR5893080", "SRX3058765", "SRS2404538", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT sphere in vivo", "dmsseq AG01043", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT sphere in vivo", "AG01043.4", "AG01043.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01043.4_R1.fastq.gz", "fastq", 633932186.0, 26698352.0, "AG01043.4 R1.fastq.gz", "0:23.74 1:0", "A:172078766;C:147459021;G:157655737;T:156729321;N:9341", 23, 0, null, null, 172078766, 147459021, 157655737, 156729321, 9341, "SRX3058765", "SRS2404538", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.62892, null, 0.12689, null, 0.76915, null, 0.59625, null, 19, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43114, "SRR5893081", "SRX3058764", "SRS2404538", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT sphere in vivo", "dmsseq AG01043", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT sphere in vivo", "AG01043.3", "AG01043.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01043.3_R1.fastq.gz", "fastq", 545501906.0, 22980935.0, "AG01043.3 R1.fastq.gz", "0:23.74 1:0", "A:147643154;C:127194084;G:135926112;T:134737007;N:1549", 23, 0, null, null, 147643154, 127194084, 135926112, 134737007, 1549, "SRX3058764", "SRS2404538", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.63069, null, 0.12544, null, 0.76781, null, 0.60018, null, 26, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43117, "SRR5893084", "SRX3058761", "SRS2404540", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq PatA WT 64c PatA DMS B2", "dmsseq pata AG01429", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq PatA WT 64c PatA DMS B2", "AG01429.1", "AG01429.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01429.1_R1.fastq.gz", "fastq", 193152200.0, 7929129.0, "AG01429.1 R1.fastq.gz", "0:24.36 1:0", "A:53713978;C:42339303;G:46822608;T:50276290;N:21", 24, 0, null, null, 53713978, 42339303, 46822608, 50276290, 21, "SRX3058761", "SRS2404540", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.69688, null, 0.0423, null, 0.76621, null, 0.51286, null, 37, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43118, "SRR5893085", "SRX3058760", "SRS2404541", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq PatA WT 64c PatA DMS B1", "dmsseq pata AG01428", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq PatA WT 64c PatA DMS B1", "AG01428.5", "AG01428.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01428.5_R1.fastq.gz", "fastq", 1471415118.0, 60775933.0, "AG01428.5 R1.fastq.gz", "0:24.21 1:0", "A:427869397;C:311916291;G:327280051;T:404336571;N:12808", 24, 0, null, null, 427869397, 311916291, 327280051, 404336571, 12808, "SRX3058760", "SRS2404541", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.69068, null, 0.05351, null, 0.76625, null, 0.51244, null, 19, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43119, "SRR5893086", "SRX3058759", "SRS2404541", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq PatA WT 64c PatA DMS B1", "dmsseq pata AG01428", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq PatA WT 64c PatA DMS B1", "AG01428.4", "AG01428.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01428.4_R1.fastq.gz", "fastq", 208326774.0, 8582890.0, "AG01428.4 R1.fastq.gz", "0:24.27 1:0", "A:60934366;C:43916600;G:46106309;T:57368748;N:751", 24, 0, null, null, 60934366, 43916600, 46106309, 57368748, 751, "SRX3058759", "SRS2404541", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.68998, null, 0.05396, null, 0.76374, null, 0.51059, null, 17, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43120, "SRR5893087", "SRX3058758", "SRS2404541", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq PatA WT 64c PatA DMS B1", "dmsseq pata AG01428", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq PatA WT 64c PatA DMS B1", "AG01428.3", "AG01428.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01428.3_R1.fastq.gz", "fastq", 201183036.0, 8321263.0, "AG01428.3 R1.fastq.gz", "0:24.18 1:0", "A:58823768;C:42490237;G:44567988;T:55298599;N:2444", 24, 0, null, null, 58823768, 42490237, 44567988, 55298599, 2444, "SRX3058758", "SRS2404541", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.6871, null, 0.05281, null, 0.76575, null, 0.51538, null, 30, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43121, "SRR5893088", "SRX3058757", "SRS2404540", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq PatA WT 64c PatA DMS B2", "dmsseq pata AG01429", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq PatA WT 64c PatA DMS B2", "AG01429.5", "AG01429.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01429.5_R1.fastq.gz", "fastq", 1025355643.0, 41973110.0, "AG01429.5 R1.fastq.gz", "0:24.43 1:0", "A:286439080;C:223476222;G:247260097;T:268171035;N:9209", 24, 0, null, null, 286439080, 223476222, 247260097, 268171035, 9209, "SRX3058757", "SRS2404540", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.69958, null, 0.04484, null, 0.76558, null, 0.51603, null, 29, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43122, "SRR5893089", "SRX3058756", "SRS2404540", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq PatA WT 64c PatA DMS B2", "dmsseq pata AG01429", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq PatA WT 64c PatA DMS B2", "AG01429.4", "AG01429.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01429.4_R1.fastq.gz", "fastq", 145578062.0, 5944282.0, "AG01429.4 R1.fastq.gz", "0:24.49 1:0", "A:40943195;C:31523692;G:34943324;T:38167309;N:542", 24, 0, null, null, 40943195, 31523692, 34943324, 38167309, 542, "SRX3058756", "SRS2404540", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.70235, null, 0.04557, null, 0.76341, null, 0.5093, null, 38, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43123, "SRR5893090", "SRX3058755", "SRS2404540", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq PatA WT 64c PatA DMS B2", "dmsseq pata AG01429", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq PatA WT 64c PatA DMS B2", "AG01429.3", "AG01429.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01429.3_R1.fastq.gz", "fastq", 140022273.0, 5737910.0, "AG01429.3 R1.fastq.gz", "0:24.40 1:0", "A:39343164;C:30378209;G:33656711;T:36642421;N:1768", 24, 0, null, null, 39343164, 30378209, 33656711, 36642421, 1768, "SRX3058755", "SRS2404540", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.69621, null, 0.04502, null, 0.764, null, 0.51161, null, 28, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43124, "SRR5893091", "SRX3058754", "SRS2404540", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq PatA WT 64c PatA DMS B2", "dmsseq pata AG01429", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq PatA WT 64c PatA DMS B2", "AG01429.2", "AG01429.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01429.2_R1.fastq.gz", "fastq", 155400644.0, 6350801.0, "AG01429.2 R1.fastq.gz", "0:24.47 1:0", "A:43541418;C:33799983;G:37361242;T:40698001;N:0", 24, 0, null, null, 43541418, 33799983, 37361242, 40698001, 0, "SRX3058754", "SRS2404540", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.70153, null, 0.04589, null, 0.76495, null, 0.51164, null, 21, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43125, "SRR5893092", "SRX3058753", "SRS2404538", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT sphere in vivo", "dmsseq AG01043", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT sphere in vivo", "AG01043.1", "AG01043.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01043.1_R1.fastq.gz", "fastq", 108747256.0, 4575669.0, "AG01043.1 R1.fastq.gz", "0:23.77 1:0", "A:29414532;C:25366431;G:27139739;T:26826074;N:480", 23, 0, null, null, 29414532, 25366431, 27139739, 26826074, 480, "SRX3058753", "SRS2404538", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.62913, null, 0.12566, null, 0.76946, null, 0.59653, null, 20, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43126, "SRR5893093", "SRX3058752", "SRS2404538", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT sphere in vivo", "dmsseq AG01043", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT sphere in vivo", "AG01043.2", "AG01043.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01043.2_R1.fastq.gz", "fastq", 37331204.0, 1581621.0, "AG01043.2 R1.fastq.gz", "0:23.60 1:0", "A:10098397;C:8686566;G:9362492;T:9181793;N:1956", 23, 0, null, null, 10098397, 8686566, 9362492, 9181793, 1956, "SRX3058752", "SRS2404538", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.60497, null, 0.12042, null, 0.77114, null, 0.5559, null, 21, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43127, "SRR5893094", "SRX3058751", "SRS2404542", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT 64c in vivo", "dmsseq AG01042", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c in vivo", "AG01042.1", "AG01042.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01042.1_R1.fastq.gz", "fastq", 126429566.0, 5343149.0, "AG01042.1 R1.fastq.gz", "0:23.66 1:0", "A:33794193;C:29213503;G:32293032;T:31128226;N:612", 23, 0, null, null, 33794193, 29213503, 32293032, 31128226, 612, "SRX3058751", "SRS2404542", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.60436, null, 0.07589, null, 0.78179, null, 0.58081, null, 23, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43128, "SRR5893095", "SRX3058750", "SRS2404542", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT 64c in vivo", "dmsseq AG01042", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c in vivo", "AG01042.2", "AG01042.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01042.2_R1.fastq.gz", "fastq", 43162881.0, 1835075.0, "AG01042.2 R1.fastq.gz", "0:23.52 1:0", "A:11533531;C:9954515;G:11073245;T:10599502;N:2088", 23, 0, null, null, 11533531, 9954515, 11073245, 10599502, 2088, "SRX3058750", "SRS2404542", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.58191, null, 0.07361, null, 0.78255, null, 0.5884, null, 27, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43129, "SRR5893096", "SRX3058749", "SRS2404532", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT 64c DMScontrol in vitro", "dmsseq AG00876", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:water in vitro|molecule:RNA|selection:pA|condition:control|replicate group:13|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c DMScontrol in vitro", "AG00876.3", "AG00876.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG00876.3_R1.fastq.gz", "fastq", 981554972.0, 12915197.0, "AG00876.3 R1.fastq.gz", "0:76", "A:261237433;C:277515571;G:240090014;T:202665429;N:46525", 76, null, null, null, 261237433, 277515571, 240090014, 202665429, 46525, "SRX3058749", "SRS2404532", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 2e-05, null, 0.0, null, 0.99995, null, 1.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43130, "SRR5893097", "SRX3058748", "SRS2404532", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT 64c DMScontrol in vitro", "dmsseq AG00876", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:water in vitro|molecule:RNA|selection:pA|condition:control|replicate group:13|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c DMScontrol in vitro", "AG00876.4", "AG00876.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG00876.4_R1.fastq.gz", "fastq", 662935688.0, 8722838.0, "AG00876.4 R1.fastq.gz", "0:76", "A:176751346;C:187148186;G:162147575;T:136873146;N:15435", 76, null, null, null, 176751346, 187148186, 162147575, 136873146, 15435, "SRX3058748", "SRS2404532", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43131, "SRR5893098", "SRX3058747", "SRS2404542", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT 64c in vivo", "dmsseq AG01042", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c in vivo", "AG01042.5", "AG01042.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01042.5_R1.fastq.gz", "fastq", 1080031154.0, 45488589.0, "AG01042.5 R1.fastq.gz", "0:23.74 1:0", "A:290744683;C:247189003;G:273714462;T:268297982;N:85024", 23, 0, null, null, 290744683, 247189003, 273714462, 268297982, 85024, "SRX3058747", "SRS2404542", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.60791, null, 0.07492, null, 0.77979, null, 0.58326, null, 29, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43132, "SRR5893099", "SRX3058746", "SRS2404542", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT 64c in vivo", "dmsseq AG01042", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c in vivo", "AG01042.6", "AG01042.6", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01042.6_R1.fastq.gz", "fastq", 283394970.0, 12033965.0, "AG01042.6 R1.fastq.gz", "0:23.55 1:0", "A:76195456;C:65114236;G:72044677;T:70039067;N:1534", 23, 0, null, null, 76195456, 65114236, 72044677, 70039067, 1534, "SRX3058746", "SRS2404542", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.59876, null, 0.07667, null, 0.78135, null, 0.58397, null, 33, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43133, "SRR5893100", "SRX3058745", "SRS2404542", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT 64c in vivo", "dmsseq AG01042", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c in vivo", "AG01042.3", "AG01042.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01042.3_R1.fastq.gz", "fastq", 635217690.0, 26879456.0, "AG01042.3 R1.fastq.gz", "0:23.63 1:0", "A:169915710;C:146718321;G:161940079;T:156641690;N:1890", 23, 0, null, null, 169915710, 146718321, 161940079, 156641690, 1890, "SRX3058745", "SRS2404542", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.60186, null, 0.07604, null, 0.78186, null, 0.58928, null, 29, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43134, "SRR5893101", "SRX3058744", "SRS2404542", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT 64c in vivo", "dmsseq AG01042", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c in vivo", "AG01042.4", "AG01042.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01042.4_R1.fastq.gz", "fastq", 737360617.0, 31187809.0, "AG01042.4 R1.fastq.gz", "0:23.64 1:0", "A:197816552;C:169921394;G:187620043;T:181992000;N:10628", 23, 0, null, null, 197816552, 169921394, 187620043, 181992000, 10628, "SRX3058744", "SRS2404542", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.60088, null, 0.07706, null, 0.78046, null, 0.547, null, 15, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43135, "SRR5893102", "SRX3058743", "SRS2404543", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT shield in vivo", "dmsseq AG01047", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT shield in vivo", "AG01047.3", "AG01047.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01047.3_R1.fastq.gz", "fastq", 688382781.0, 30034225.0, "AG01047.3 R1.fastq.gz", "0:22.92 1:0", "A:189019980;C:152064230;G:163028336;T:184268177;N:2058", 22, 0, null, null, 189019980, 152064230, 163028336, 184268177, 2058, "SRX3058743", "SRS2404543", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.57527, null, 0.14405, null, 0.7892, null, 0.59515, null, 16, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43136, "SRR5893103", "SRX3058742", "SRS2404543", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT shield in vivo", "dmsseq AG01047", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT shield in vivo", "AG01047.4", "AG01047.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01047.4_R1.fastq.gz", "fastq", 786863431.0, 34313776.0, "AG01047.4 R1.fastq.gz", "0:22.93 1:0", "A:216579236;C:173455382;G:185880723;T:210944466;N:3624", 22, 0, null, null, 216579236, 173455382, 185880723, 210944466, 3624, "SRX3058742", "SRS2404543", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.57576, null, 0.14501, null, 0.79026, null, 0.5962, null, 25, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43137, "SRR5893104", "SRX3058741", "SRS2404544", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT 64c in vivo", "dmsseq AG01046", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c in vivo", "AG01046.1", "AG01046.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01046.1_R1.fastq.gz", "fastq", 104571264.0, 4565699.0, "AG01046.1 R1.fastq.gz", "0:22.90 1:0", "A:26920338;C:24177052;G:26506298;T:26967196;N:380", 22, 0, null, null, 26920338, 24177052, 26506298, 26967196, 380, "SRX3058741", "SRS2404544", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.5641, null, 0.06574, null, 0.78437, null, 0.58268, null, 15, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43138, "SRR5893105", "SRX3058740", "SRS2404544", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT 64c in vivo", "dmsseq AG01046", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c in vivo", "AG01046.2", "AG01046.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01046.2_R1.fastq.gz", "fastq", 34508189.0, 1516870.0, "AG01046.2 R1.fastq.gz", "0:22.75 1:0", "A:8891670;C:7954125;G:8796911;T:8864593;N:890", 22, 0, null, null, 8891670, 7954125, 8796911, 8864593, 890, "SRX3058740", "SRS2404544", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.54153, null, 0.06305, null, 0.7852, null, 0.5792, null, 19, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43139, "SRR5893106", "SRX3058739", "SRS2404544", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT 64c in vivo", "dmsseq AG01046", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c in vivo", "AG01046.3", "AG01046.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01046.3_R1.fastq.gz", "fastq", 559711334.0, 24457578.0, "AG01046.3 R1.fastq.gz", "0:22.88 1:0", "A:144168923;C:129246711;G:141668875;T:144625154;N:1671", 22, 0, null, null, 144168923, 129246711, 141668875, 144625154, 1671, "SRX3058739", "SRS2404544", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.56488, null, 0.06449, null, 0.7838, null, 0.57611, null, 20, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43140, "SRR5893107", "SRX3058738", "SRS2404544", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT 64c in vivo", "dmsseq AG01046", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c in vivo", "AG01046.4", "AG01046.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01046.4_R1.fastq.gz", "fastq", 639006387.0, 27909373.0, "AG01046.4 R1.fastq.gz", "0:22.90 1:0", "A:165043321;C:147246240;G:161359572;T:165354476;N:2778", 22, 0, null, null, 165043321, 147246240, 161359572, 165354476, 2778, "SRX3058738", "SRS2404544", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.56251, null, 0.06604, null, 0.78417, null, 0.57986, null, 18, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43141, "SRR5893108", "SRX3058737", "SRS2404544", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT 64c in vivo", "dmsseq AG01046", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c in vivo", "AG01046.5", "AG01046.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01046.5_R1.fastq.gz", "fastq", 810814539.0, 35324852.0, "AG01046.5 R1.fastq.gz", "0:22.95 1:0", "A:209392559;C:186085613;G:205018734;T:210262020;N:55613", 22, 0, null, null, 209392559, 186085613, 205018734, 210262020, 55613, "SRX3058737", "SRS2404544", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.57046, null, 0.06498, null, 0.78423, null, 0.5699, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43142, "SRR5893109", "SRX3058736", "SRS2404544", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT 64c in vivo", "dmsseq AG01046", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c in vivo", "AG01046.6", "AG01046.6", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01046.6_R1.fastq.gz", "fastq", 364856161.0, 16004319.0, "AG01046.6 R1.fastq.gz", "0:22.80 1:0", "A:94562115;C:83891926;G:92182690;T:94217438;N:1992", 22, 0, null, null, 94562115, 83891926, 92182690, 94217438, 1992, "SRX3058736", "SRS2404544", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.56018, null, 0.06351, null, 0.78421, null, 0.58178, null, 15, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43143, "SRR5893110", "SRX3058735", "SRS2404543", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT shield in vivo", "dmsseq AG01047", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT shield in vivo", "AG01047.1", "AG01047.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01047.1_R1.fastq.gz", "fastq", 128687784.0, 5609452.0, "AG01047.1 R1.fastq.gz", "0:22.94 1:0", "A:35296614;C:28459568;G:30549212;T:34381876;N:514", 22, 0, null, null, 35296614, 28459568, 30549212, 34381876, 514, "SRX3058735", "SRS2404543", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.5755, null, 0.144, null, 0.7907, null, 0.59285, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43144, "SRR5893111", "SRX3058734", "SRS2404543", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT shield in vivo", "dmsseq AG01047", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT shield in vivo", "AG01047.2", "AG01047.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01047.2_R1.fastq.gz", "fastq", 42440299.0, 1862352.0, "AG01047.2 R1.fastq.gz", "0:22.79 1:0", "A:11644782;C:9368619;G:10136237;T:11289519;N:1142", 22, 0, null, null, 11644782, 9368619, 10136237, 11289519, 1142, "SRX3058734", "SRS2404543", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.55293, null, 0.13885, null, 0.79379, null, 0.59223, null, 15, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43145, "SRR5893112", "SRX3058733", "SRS2404545", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT sphere in vivo", "dmsseq AG01049", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT sphere in vivo", "AG01049.4", "AG01049.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01049.4_R1.fastq.gz", "fastq", 693084196.0, 30220927.0, "AG01049.4 R1.fastq.gz", "0:22.93 1:0", "A:184260362;C:156379835;G:169790720;T:182650190;N:3089", 22, 0, null, null, 184260362, 156379835, 169790720, 182650190, 3089, "SRX3058733", "SRS2404545", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.56552, null, 0.10478, null, 0.77329, null, 0.58948, null, 15, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43146, "SRR5893113", "SRX3058732", "SRS2404545", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT sphere in vivo", "dmsseq AG01049", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT sphere in vivo", "AG01049.3", "AG01049.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01049.3_R1.fastq.gz", "fastq", 605892767.0, 26434367.0, "AG01049.3 R1.fastq.gz", "0:22.92 1:0", "A:160713810;C:136961096;G:148749325;T:159466624;N:1912", 22, 0, null, null, 160713810, 136961096, 148749325, 159466624, 1912, "SRX3058732", "SRS2404545", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.5625, null, 0.10811, null, 0.77224, null, 0.58777, null, 23, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43147, "SRR5893114", "SRX3058731", "SRS2404545", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT sphere in vivo", "dmsseq AG01049", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT sphere in vivo", "AG01049.6", "AG01049.6", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01049.6_R1.fastq.gz", "fastq", 394478885.0, 17274979.0, "AG01049.6 R1.fastq.gz", "0:22.84 1:0", "A:105227778;C:88892938;G:96681477;T:103674703;N:1989", 22, 0, null, null, 105227778, 88892938, 96681477, 103674703, 1989, "SRX3058731", "SRS2404545", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.55998, null, 0.10523, null, 0.77279, null, 0.58664, null, 29, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43148, "SRR5893115", "SRX3058730", "SRS2404545", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT sphere in vivo", "dmsseq AG01049", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT sphere in vivo", "AG01049.5", "AG01049.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01049.5_R1.fastq.gz", "fastq", 886753255.0, 38566196.0, "AG01049.5 R1.fastq.gz", "0:22.99 1:0", "A:235539511;C:199422326;G:217573523;T:234156689;N:61206", 22, 0, null, null, 235539511, 199422326, 217573523, 234156689, 61206, "SRX3058730", "SRS2404545", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.56676, null, 0.10782, null, 0.77331, null, 0.58475, null, 25, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43149, "SRR5893116", "SRX3058729", "SRS2404543", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT shield in vivo", "dmsseq AG01047", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT shield in vivo", "AG01047.6", "AG01047.6", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01047.6_R1.fastq.gz", "fastq", 450514845.0, 19728387.0, "AG01047.6 R1.fastq.gz", "0:22.84 1:0", "A:124287698;C:99171890;G:106632738;T:120420206;N:2313", 22, 0, null, null, 124287698, 99171890, 106632738, 120420206, 2313, "SRX3058729", "SRS2404543", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.57005, null, 0.14316, null, 0.78806, null, 0.59387, null, 15, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43150, "SRR5893117", "SRX3058728", "SRS2404543", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT shield in vivo", "dmsseq AG01047", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT shield in vivo", "AG01047.5", "AG01047.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01047.5_R1.fastq.gz", "fastq", 1004009476.0, 43664444.0, "AG01047.5 R1.fastq.gz", "0:22.99 1:0", "A:276219561;C:220490343;G:237521478;T:269709007;N:69087", 22, 0, null, null, 276219561, 220490343, 237521478, 269709007, 69087, "SRX3058728", "SRS2404543", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.57878, null, 0.14525, null, 0.78841, null, 0.58513, null, 28, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43151, "SRR5893118", "SRX3058727", "SRS2404545", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT sphere in vivo", "dmsseq AG01049", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT sphere in vivo", "AG01049.2", "AG01049.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01049.2_R1.fastq.gz", "fastq", 37381210.0, 1641906.0, "AG01049.2 R1.fastq.gz", "0:22.77 1:0", "A:9910821;C:8448316;G:9246060;T:9775054;N:959", 22, 0, null, null, 9910821, 8448316, 9246060, 9775054, 959, "SRX3058727", "SRS2404545", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.54348, null, 0.10292, null, 0.77467, null, 0.59127, null, 21, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43152, "SRR5893119", "SRX3058726", "SRS2404545", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq WT sphere in vivo", "dmsseq AG01049", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT sphere in vivo", "AG01049.1", "AG01049.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01049.1_R1.fastq.gz", "fastq", 113060119.0, 4927027.0, "AG01049.1 R1.fastq.gz", "0:22.95 1:0", "A:29961989;C:25583869;G:27802427;T:29711326;N:508", 22, 0, null, null, 29961989, 25583869, 27802427, 29711326, 508, "SRX3058726", "SRS2404545", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.56357, null, 0.10878, null, 0.77143, null, 0.59024, null, 23, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43153, "SRR5893120", "SRX3058725", "SRS2404546", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq IVT 64c B2", "dmsseq AG01269", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq IVT 64c B2", "AG01269.2", "AG01269.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01269.2_R1.fastq.gz", "fastq", 615648941.0, 27257391.0, "AG01269.2 R1.fastq.gz", "0:22.59 1:0", "A:163885634;C:143593857;G:157437520;T:150675530;N:56400", 22, 0, null, null, 163885634, 143593857, 157437520, 150675530, 56400, "SRX3058725", "SRS2404546", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.6277, null, 0.07639, null, 0.78236, null, 0.60487, null, 20, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43154, "SRR5893121", "SRX3058724", "SRS2404546", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq IVT 64c B2", "dmsseq AG01269", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq IVT 64c B2", "AG01269.1", "AG01269.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01269.1_R1.fastq.gz", "fastq", 461341500.0, 20486790.0, "AG01269.1 R1.fastq.gz", "0:22.52 1:0", "A:122338299;C:107915972;G:118163678;T:112917569;N:5982", 22, 0, null, null, 122338299, 107915972, 118163678, 112917569, 5982, "SRX3058724", "SRS2404546", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.62415, null, 0.07628, null, 0.78133, null, 0.60032, null, 19, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43155, "SRR8782107", "SRX3058723", "SRS2404547", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA 6h pA RNA B5", "miniresa AG01735", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:26|replicate:5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA 6h pA RNA B5", "AG01735.1", "AG01735.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "SRR5893122_replace_R1.fastq.gz", "fastq", 172767228.0, 2273253.0, "SRR5893122 replace R1.fastq.gz", "0:76", "A:46635317;C:32625014;G:34801109;T:58688753;N:17035", 76, null, null, null, 46635317, 32625014, 34801109, 58688753, 17035, "SRX3058723", "SRS2404547", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.94143, null, 2e-05, null, 0.99768, null, 0.61729, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-03-25", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43156, "SRR8782106", "SRX3058722", "SRS2404548", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA 6h pA RNA B4", "miniresa AG01734", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:26|replicate:4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA 6h pA RNA B4", "AG01734.1", "AG01734.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "SRR5893123_replace_R1.fastq.gz", "fastq", 162402500.0, 2136875.0, "SRR5893123 replace R1.fastq.gz", "0:76", "A:43702648;C:30815303;G:32732910;T:55135738;N:15901", 76, null, null, null, 43702648, 30815303, 32732910, 55135738, 15901, "SRX3058722", "SRS2404548", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.94147, null, 0.0, null, 0.99791, null, 0.62083, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-03-25", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43157, "SRR8782105", "SRX3058721", "SRS2404549", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA 6h a Am pA RNA B4", "miniresa AG01740", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|replicate group:27|replicate:4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA 6h a Am pA RNA B4", "AG01740.1", "AG01740.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "SRR5893124_replace_R1.fastq.gz", "fastq", 155277424.0, 2043124.0, "SRR5893124 replace R1.fastq.gz", "0:76", "A:41889716;C:29676013;G:31219225;T:52477242;N:15228", 76, null, null, null, 41889716, 29676013, 31219225, 52477242, 15228, "SRX3058721", "SRS2404549", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.94462, null, 1e-05, null, 0.99772, null, 0.61448, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-03-25", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43158, "SRR8782103", "SRX3058720", "SRS2404550", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA 6h a Am pA RNA B3", "miniresa AG01739", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|replicate group:27|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA 6h a Am pA RNA B3", "AG01739.1", "AG01739.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "SRR5893125_replace_R1.fastq.gz", "fastq", 141372692.0, 1860167.0, "SRR5893125 replace R1.fastq.gz", "0:76", "A:38036177;C:26891347;G:28463167;T:47966401;N:15600", 76, null, null, null, 38036177, 26891347, 28463167, 47966401, 15600, "SRX3058720", "SRS2404550", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.94098, null, 2e-05, null, 0.99772, null, 0.59143, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-03-25", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43159, "SRR8782100", "SRX3058719", "SRS2404551", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. 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