{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Cleavage\" and experiment.library_selection = \"unspecified\"", "rows": [[8055, "ERR022484", "ERX008924", "ERS017427", "ERP000400", "PRJEB2333", "Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer", "E-MTAB-434", "Other", null, null, null, null, "E MTAB 434:ZF 2cells", "SAMEA898400", "Wellcome Sanger Institute", "Alias:E MTAB 434:ZF 2cells|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 03 10T17:55:05Z|INSDC last update:2018 03 08T15:25:14Z|INSDC status:public|SRA accession:ERS017427|Sample Name:ERS017427|Sex:mixed|StrainOrLine:Tuebingen|Title:ZF 2cells", null, null, null, null, null, null, null, null, "Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer", "E MTAB 434:sequencing of Zebrafish embryo 2cells", "RNA from Zebrafish embryo 2cells", "Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer", "Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.", "Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:cell", "FL-cDNA", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer II", null, "ERP000400", "Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer", "ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16", "4946_5.srf", "srf", 3947547008.0, 25970704.0, "E MTAB 434:4946 5.srf", "0:76 1:76", "A:1069302461;C:914233601;G:902631356;T:1055986090;N:5393500", 76, 76, null, null, 1069302461, 914233601, 902631356, 1055986090, 5393500, "ERX008924", "ERS017427", "ERA015179", "SC|Wellcome Trust Sanger Institute", "SC|Wellcome Trust Sanger Institute", 2, 0.93356, 0.93346, 0.03988, 0.04022, 0.79135, 0.79198, 0.48864, 0.48464, 76, 76, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2011-03-10", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36408, "SRR546817", "SRX180747", "SRS358988", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain embryo 2 cells stage", "D. rerio 2 cells embryo", "D. rerio 2 cells embryo", null, null, null, null, null, null, null, null, null, null, "RNAseq D. rerio 2 cells embryo", "RNAseq D. rerio 2 cells embryo", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", "1520Application ReadForward11Application ReadReverse77", "SRP013950", null, null, null, null, 2799828144.0, 18419922.0, "RNAseq D. rerio 2 cells embryo", "0:76 1:76", "A:678251421;C:711410510;G:729905459;T:677312772;N:2947982", 76, 76, null, null, 678251421, 711410510, 729905459, 677312772, 2947982, "SRX180747", "SRS358988", "SRA055273", "University of Bergen", "ZEPROME consortium", 2, 0.9498, 0.94704, 0.02363, 0.02442, 0.7988, 0.80221, 0.48657, 0.49361, 76, 76, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2015-07-22", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36761, "SRR10295266", "SRX7008094", "SRS431105", "SRP023492", "PRJNA206070", "Nanog SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition", "GSE47558", "Other", "Upon fertilization maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT a universal step in animal development unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish ZGA is required for gastrulation and clearance of maternal mRNAs which is achieved in part by the conserved microRNA miR 430. However the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation and a failure to activate >75% of zygotic genes. Furthermore we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre and post MZT; ribosome profiling pre MZT", null, "pubmed:24056933", null, "WT 2hpf Total mRNA", "GSM1152440", null, "source name:WT 2hpf Total mRNA|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA", null, null, null, null, null, null, null, null, "WT 64c R0", "AGR000324", "AGR000324", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP023492", null, null, "AGR000324_R1.fastq.gz", "fastq", 781504124.0, 10282949.0, "AGR000324 R1.fastq.gz", "0:76", "A:151879560;C:240178928;G:220957551;T:168456166;N:31919", 76, null, null, null, 151879560, 240178928, 220957551, 168456166, 31919, "SRX7008094", "SRS431105", "SRA980383", "Yale_Giraldez|Genetics", "Giraldez Lab, Genetics, Yale University", 1, 0.88875, null, 0.14141, null, 0.796, null, 0.72154, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-10-16", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [41391, "SRR4375176", "SRX2226710", "SRS1732686", "SRP090954", "PRJNA345638", "RESA identifies mRNA regulatory sequences with high resolution", "PRJNA345638", "Other", "Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.", null, null, null, "RESA Seq WT 64c pA r3 B2", "resa AG01061", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA Seq WT 64c pA r3 B2", "AG01061.1", "AG01061.1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090954", null, null, "AG01061.1_R1.fastq.gz AG01061.1_R2.fastq.gz", "fastq fastq", 724448416.0, 4766108.0, "AG01061.1 R2.fastq.gz", "0:76 1:76", "A:224701149;C:138989041;G:139762199;T:220977796;N:18231", 76, 76, null, null, 224701149, 138989041, 139762199, 220977796, 18231, "SRX2226710", "SRS1732686", "SRA482696", "Yale University|Genetics", "Yale University", 2, 0.84913, 0.84756, 0.03557, 0.03568, 0.97153, 0.97116, 0.47281, 0.46157, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41402, "SRR4375094", "SRX2226666", "SRS1732677", "SRP090954", "PRJNA345638", "RESA identifies mRNA regulatory sequences with high resolution", "PRJNA345638", "Other", "Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.", null, null, null, "RESA Seq WT 64c pA r3 B1", "resa AG01060", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA Seq WT 64c pA r3 B1", "AG01060.1", "AG01060.1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090954", null, null, "AG01060.1_R1.fastq.gz AG01060.1_R2.fastq.gz", "fastq fastq", 531097120.0, 3494060.0, "AG01060.1 R1.fastq.gz", "0:76 1:76", "A:164891814;C:101739900;G:102440303;T:162011179;N:13924", 76, 76, null, null, 164891814, 101739900, 102440303, 162011179, 13924, "SRX2226666", "SRS1732677", "SRA482696", "Yale University|Genetics", "Yale University", 2, 0.84523, 0.84587, 0.03561, 0.03503, 0.9723, 0.97161, 0.46204, 0.47901, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-12-31", "Cleavage", "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"], [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"], [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"], [43099, "SRR5893058", "SRX3058787", "SRS2404528", "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, "mRNA Seq R0 patA WT 64c PatA RPF input B2", "mrna seq pata AG01431", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:PatA|molecule:RNA|selection:r0|condition:input|replicate group:23|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA Seq R0 patA WT 64c PatA RPF input B2", "AG01431.1", "AG01431.1", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01431.1_R1.fastq.gz", "fastq", 935580824.0, 12310274.0, "AG01431.1 R1.fastq.gz", "0:76", "A:188726598;C:276745094;G:258235229;T:211815415;N:58488", 76, null, null, null, 188726598, 276745094, 258235229, 211815415, 58488, "SRX3058787", "SRS2404528", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.89193, null, 0.09644, null, 0.7849, null, 0.69832, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43100, "SRR5893059", "SRX3058786", "SRS2404528", "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, "mRNA Seq R0 patA WT 64c PatA RPF input B2", "mrna seq pata AG01431", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:PatA|molecule:RNA|selection:r0|condition:input|replicate group:23|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA Seq R0 patA WT 64c PatA RPF input B2", "AG01431.2", "AG01431.2", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01431.2_R1.fastq.gz", "fastq", 2550535528.0, 33559678.0, "AG01431.2 R1.fastq.gz", "0:76", "A:541016830;C:720948568;G:664552003;T:623742439;N:275688", 76, null, null, null, 541016830, 720948568, 664552003, 623742439, 275688, "SRX3058786", "SRS2404528", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.90466, null, 0.10321, null, 0.77595, null, 0.60561, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43101, "SRR5893060", "SRX3058785", "SRS2404530", "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, "mRNA Seq R0 patA WT 64c RPF input B1", "mrna seq pata AG01432", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:r0|condition:input|replicate group:24|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA Seq R0 patA WT 64c RPF input B1", "AG01432.1", "AG01432.1", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01432.1_R1.fastq.gz", "fastq", 2796444700.0, 36795325.0, "AG01432.1 R1.fastq.gz", "0:76", "A:663756831;C:716464328;G:666812843;T:749363967;N:46731", 76, null, null, null, 663756831, 716464328, 666812843, 749363967, 46731, "SRX3058785", "SRS2404530", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.85828, null, 0.09273, null, 0.75534, null, 0.50507, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43102, "SRR5893061", "SRX3058784", "SRS2404531", "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, "mRNA Seq R0 patA WT 64c RPF input B2", "mrna seq pata AG01433", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:r0|condition:input|replicate group:24|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA Seq R0 patA WT 64c RPF input B2", "AG01433.1", "AG01433.1", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01433.1_R1.fastq.gz", "fastq", 3208682532.0, 42219507.0, "AG01433.1 R1.fastq.gz", "0:76", "A:715292036;C:869176418;G:807214698;T:816945712;N:53668", 76, null, null, null, 715292036, 869176418, 807214698, 816945712, 53668, "SRX3058784", "SRS2404531", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.85439, null, 0.09801, null, 0.76597, null, 0.58538, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "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"], [43115, "SRR5893082", "SRX3058763", "SRS2404539", "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, "mRNA Seq R0 patA WT 64c PatA RPF input B1", "mrna seq pata AG01430", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:PatA|molecule:RNA|selection:r0|condition:input|replicate group:23|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA Seq R0 patA WT 64c PatA RPF input B1", "AG01430.2", "AG01430.2", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01430.2_R1.fastq.gz", "fastq", 3133028560.0, 41224060.0, "AG01430.2 R1.fastq.gz", "0:76", "A:672361176;C:875054552;G:808035984;T:777238497;N:338351", 76, null, null, null, 672361176, 875054552, 808035984, 777238497, 338351, "SRX3058763", "SRS2404539", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.88898, null, 0.09238, null, 0.77234, null, 0.6234, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43116, "SRR5893083", "SRX3058762", "SRS2404539", "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, "mRNA Seq R0 patA WT 64c PatA RPF input B1", "mrna seq pata AG01430", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:PatA|molecule:RNA|selection:r0|condition:input|replicate group:23|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA Seq R0 patA WT 64c PatA RPF input B1", "AG01430.1", "AG01430.1", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01430.1_R1.fastq.gz", "fastq", 898114724.0, 11817299.0, "AG01430.1 R1.fastq.gz", "0:76", "A:187456862;C:260421633;G:242938837;T:207239930;N:57462", 76, null, null, null, 187456862, 260421633, 242938837, 207239930, 57462, "SRX3058762", "SRS2404539", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.87315, null, 0.08685, null, 0.78117, null, 0.65305, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-08-03", "Cleavage", "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"], [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"], [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"], [43172, "SRR5893139", "SRX3058706", "SRS2404557", "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 CHX B1", "dmsseq AG01273", null, "strain:TU/AB|age:2.0|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|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c CHX B1", "AG01273.1", "AG01273.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01273.1_R1.fastq.gz", "fastq", 205385355.0, 9210408.0, "AG01273.1 R1.fastq.gz", "0:22.30 1:0", "A:55663483;C:47328873;G:50322223;T:52066694;N:4082", 22, 0, null, null, 55663483, 47328873, 50322223, 52066694, 4082, "SRX3058706", "SRS2404557", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.60509, null, 0.06208, null, 0.78417, null, 0.57855, null, 26, 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"], [43173, "SRR5893140", "SRX3058705", "SRS2404557", "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 CHX B1", "dmsseq AG01273", null, "strain:TU/AB|age:2.0|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|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c CHX B1", "AG01273.2", "AG01273.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01273.2_R1.fastq.gz", "fastq", 187794014.0, 8402532.0, "AG01273.2 R1.fastq.gz", "0:22.35 1:0", "A:51237074;C:43080418;G:45763165;T:47701058;N:12299", 22, 0, null, null, 51237074, 43080418, 45763165, 47701058, 12299, "SRX3058705", "SRS2404557", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.60944, null, 0.06401, null, 0.78393, null, 0.58071, 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"], [43174, "SRR5893141", "SRX3058704", "SRS2404558", "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, "RPF patA WT 64c PatA RPF B2", "ribo seq pata AG01412", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:cyclohex PatA|molecule:RNA|condition:RPF 28nt|replicate group:20|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RPF patA WT 64c PatA RPF B2", "AG01412.1", "AG01412.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01412.1_R1.fastq.gz", "fastq", 2162256802.0, 75040267.0, "AG01412.1 R1.fastq.gz", "0:28.81 1:0", "A:347363501;C:619335399;G:838844065;T:356708961;N:4876", 28, 0, null, null, 347363501, 619335399, 838844065, 356708961, 4876, "SRX3058704", "SRS2404558", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.97696, null, 0.23102, null, 0.98936, null, 0.86543, 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"], [43175, "SRR5893142", "SRX3058703", "SRS2404559", "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, "RPF patA WT 64c PatA RPF B1", "ribo seq pata AG01411", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:cyclohex PatA|molecule:RNA|condition:RPF 28nt|replicate group:20|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RPF patA WT 64c PatA RPF B1", "AG01411.1", "AG01411.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01411.1_R1.fastq.gz", "fastq", 1910107983.0, 66035087.0, "AG01411.1 R1.fastq.gz", "0:28.93 1:0", "A:300687332;C:552860495;G:739754137;T:316801751;N:4268", 28, 0, null, null, 300687332, 552860495, 739754137, 316801751, 4268, "SRX3058703", "SRS2404559", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.97889, null, 0.23202, null, 0.98924, null, 0.90161, null, 25, 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"], [43176, "SRR5893143", "SRX3058702", "SRS2404560", "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 CHX B2", "dmsseq AG01274", null, "strain:TU/AB|age:2.0|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:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c CHX B2", "AG01274.2", "AG01274.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01274.2_R1.fastq.gz", "fastq", 459461300.0, 20542141.0, "AG01274.2 R1.fastq.gz", "0:22.37 1:0", "A:124126012;C:105390527;G:112976938;T:116937505;N:30318", 22, 0, null, null, 124126012, 105390527, 112976938, 116937505, 30318, "SRX3058702", "SRS2404560", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.59447, null, 0.06348, null, 0.7821, null, 0.57589, 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"], [43177, "SRR5893144", "SRX3058701", "SRS2404560", "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 CHX B2", "dmsseq AG01274", null, "strain:TU/AB|age:2.0|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:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c CHX B2", "AG01274.1", "AG01274.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01274.1_R1.fastq.gz", "fastq", 501597363.0, 22476461.0, "AG01274.1 R1.fastq.gz", "0:22.32 1:0", "A:134700192;C:115536878;G:123965600;T:127384648;N:10045", 22, 0, null, null, 134700192, 115536878, 123965600, 127384648, 10045, "SRX3058701", "SRS2404560", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.59298, null, 0.06256, null, 0.78344, null, 0.57219, 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"], [43178, "SRR5893145", "SRX3058700", "SRS2404557", "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 CHX B1", "dmsseq AG01273", null, "strain:TU/AB|age:2.0|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|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c CHX B1", "AG01273.4", "AG01273.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01273.4_R1.fastq.gz", "fastq", 550272586.0, 24602706.0, "AG01273.4 R1.fastq.gz", "0:22.37 1:0", "A:149890969;C:126475050;G:134175640;T:139701774;N:29153", 22, 0, null, null, 149890969, 126475050, 134175640, 139701774, 29153, "SRX3058700", "SRS2404557", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.61101, null, 0.06398, null, 0.78324, null, 0.57945, 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"], [43179, "SRR5893146", "SRX3058699", "SRS2404557", "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 CHX B1", "dmsseq AG01273", null, "strain:TU/AB|age:2.0|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|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c CHX B1", "AG01273.3", "AG01273.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01273.3_R1.fastq.gz", "fastq", 54904714.0, 2452933.0, "AG01273.3 R1.fastq.gz", "0:22.38 1:0", "A:15008668;C:12562628;G:13368072;T:13965169;N:177", 22, 0, null, null, 15008668, 12562628, 13368072, 13965169, 177, "SRX3058699", "SRS2404557", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.61211, null, 0.06366, null, 0.78421, null, 0.57817, 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"], [43180, "SRR5893147", "SRX3058698", "SRS2404564", "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, "RPF patA WT 64c RPF B2", "ribo seq pata AG01410", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:cyclohex|molecule:RNA|condition:RPF 28nt|replicate group:19|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RPF patA WT 64c RPF B2", "AG01410.1", "AG01410.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01410.1_R1.fastq.gz", "fastq", 896457606.0, 30924822.0, "AG01410.1 R1.fastq.gz", "0:28.99 1:0", "A:143467171;C:256011945;G:344023285;T:152953270;N:1935", 28, 0, null, null, 143467171, 256011945, 344023285, 152953270, 1935, "SRX3058698", "SRS2404564", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.97092, null, 0.22415, null, 0.95327, null, 0.90171, 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"], [43181, "SRR5893148", "SRX3058697", "SRS2404568", "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, "RPF patA WT 64c RPF B1", "ribo seq pata AG01409", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:cyclohex|molecule:RNA|condition:RPF 28nt|replicate group:19|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RPF patA WT 64c RPF B1", "AG01409.1", "AG01409.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01409.1_R1.fastq.gz", "fastq", 938684699.0, 32529082.0, "AG01409.1 R1.fastq.gz", "0:28.86 1:0", "A:142126680;C:274644625;G:363605768;T:158305494;N:2132", 28, 0, null, null, 142126680, 274644625, 363605768, 158305494, 2132, "SRX3058697", "SRS2404568", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.97397, null, 0.20971, null, 0.95004, null, 0.84231, 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"], [43182, "SRR5893149", "SRX3058696", "SRS2404560", "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 CHX B2", "dmsseq AG01274", null, "strain:TU/AB|age:2.0|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:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c CHX B2", "AG01274.4", "AG01274.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01274.4_R1.fastq.gz", "fastq", 1344534454.0, 60059214.0, "AG01274.4 R1.fastq.gz", "0:22.39 1:0", "A:362915405;C:308811924;G:330761212;T:341975353;N:70560", 22, 0, null, null, 362915405, 308811924, 330761212, 341975353, 70560, "SRX3058696", "SRS2404560", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.59958, null, 0.0635, null, 0.7838, null, 0.56804, null, 26, 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"], [43183, "SRR5893150", "SRX3058695", "SRS2404560", "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 CHX B2", "dmsseq AG01274", null, "strain:TU/AB|age:2.0|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:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq WT 64c CHX B2", "AG01274.3", "AG01274.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01274.3_R1.fastq.gz", "fastq", 134313194.0, 5995068.0, "AG01274.3 R1.fastq.gz", "0:22.40 1:0", "A:36360107;C:30693939;G:33046295;T:34212398;N:455", 22, 0, null, null, 36360107, 30693939, 33046295, 34212398, 455, "SRX3058695", "SRS2404560", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.59783, null, 0.06446, null, 0.78238, null, 0.56192, 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"], [43184, "SRR5893151", "SRX3058694", "SRS2404569", "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 DMS B2", "dmsseq pata AG01427", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq PatA WT 64c DMS B2", "AG01427.1", "AG01427.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01427.1_R1.fastq.gz", "fastq", 66167485.0, 2702406.0, "AG01427.1 R1.fastq.gz", "0:24.48 1:0", "A:18811218;C:14362315;G:15330666;T:17663280;N:6", 24, 0, null, null, 18811218, 14362315, 15330666, 17663280, 6, "SRX3058694", "SRS2404569", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.64942, null, 0.04191, null, 0.7698, null, 0.51098, 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"], [43185, "SRR5893152", "SRX3058693", "SRS2404569", "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 DMS B2", "dmsseq pata AG01427", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq PatA WT 64c DMS B2", "AG01427.2", "AG01427.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01427.2_R1.fastq.gz", "fastq", 67139641.0, 2738361.0, "AG01427.2 R1.fastq.gz", "0:24.52 1:0", "A:19342582;C:14342887;G:15340438;T:18113565;N:169", 24, 0, null, null, 19342582, 14342887, 15340438, 18113565, 169, "SRX3058693", "SRS2404569", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.65215, null, 0.04753, null, 0.76883, null, 0.5104, null, 16, 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"], [43186, "SRR5893153", "SRX3058692", "SRS2404569", "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 DMS B2", "dmsseq pata AG01427", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq PatA WT 64c DMS B2", "AG01427.3", "AG01427.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01427.3_R1.fastq.gz", "fastq", 704767851.0, 28828044.0, "AG01427.3 R1.fastq.gz", "0:24.45 1:0", "A:203637610;C:150293192;G:160683763;T:190140606;N:12680", 24, 0, null, null, 203637610, 150293192, 160683763, 190140606, 12680, "SRX3058692", "SRS2404569", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.64933, null, 0.04611, null, 0.76769, null, 0.51439, 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"], [43187, "SRR5893154", "SRX3058691", "SRS2404569", "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 DMS B2", "dmsseq pata AG01427", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq PatA WT 64c DMS B2", "AG01427.4", "AG01427.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01427.4_R1.fastq.gz", "fastq", 1000317078.0, 40966065.0, "AG01427.4 R1.fastq.gz", "0:24.42 1:0", "A:287346729;C:214437026;G:228974386;T:269545470;N:13467", 24, 0, null, null, 287346729, 214437026, 228974386, 269545470, 13467, "SRX3058691", "SRS2404569", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.64386, null, 0.04612, null, 0.76962, null, 0.5135, 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"], [43188, "SRR5893155", "SRX3058690", "SRS2404570", "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 DMS B1", "dmsseq pata AG01426", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq PatA WT 64c DMS B1", "AG01426.1", "AG01426.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01426.1_R1.fastq.gz", "fastq", 55216827.0, 2272440.0, "AG01426.1 R1.fastq.gz", "0:24.30 1:0", "A:15961884;C:11761582;G:12384264;T:15109092;N:5", 24, 0, null, null, 15961884, 11761582, 12384264, 15109092, 5, "SRX3058690", "SRS2404570", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.63792, null, 0.04462, null, 0.7699, null, 0.50858, null, 16, 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"], [43189, "SRR5893156", "SRX3058689", "SRS2404570", "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 DMS B1", "dmsseq pata AG01426", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq PatA WT 64c DMS B1", "AG01426.2", "AG01426.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01426.2_R1.fastq.gz", "fastq", 55603889.0, 2285413.0, "AG01426.2 R1.fastq.gz", "0:24.33 1:0", "A:16361036;C:11633883;G:12264363;T:15344485;N:122", 24, 0, null, null, 16361036, 11633883, 12264363, 15344485, 122, "SRX3058689", "SRS2404570", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.64013, null, 0.05074, null, 0.7679, null, 0.51128, null, 26, 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"], [43190, "SRR5893157", "SRX3058688", "SRS2404570", "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 DMS B1", "dmsseq pata AG01426", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq PatA WT 64c DMS B1", "AG01426.3", "AG01426.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01426.3_R1.fastq.gz", "fastq", 582810380.0, 24022113.0, "AG01426.3 R1.fastq.gz", "0:24.26 1:0", "A:171923667;C:121497225;G:128382139;T:160996861;N:10488", 24, 0, null, null, 171923667, 121497225, 128382139, 160996861, 10488, "SRX3058688", "SRS2404570", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.63415, null, 0.04941, null, 0.76966, null, 0.51507, 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"], [43191, "SRR5893158", "SRX3058687", "SRS2404570", "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 DMS B1", "dmsseq pata AG01426", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq PatA WT 64c DMS B1", "AG01426.4", "AG01426.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01426.4_R1.fastq.gz", "fastq", 825030738.0, 34044199.0, "AG01426.4 R1.fastq.gz", "0:24.23 1:0", "A:242347827;C:172817407;G:182427615;T:227426785;N:11104", 24, 0, null, null, 242347827, 172817407, 182427615, 227426785, 11104, "SRX3058687", "SRS2404570", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.62999, null, 0.04967, null, 0.77013, null, 0.51317, 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"], [43192, "SRR5893159", "SRX3058686", "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", "AG01428.1", "AG01428.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01428.1_R1.fastq.gz", "fastq", 276904338.0, 11469969.0, "AG01428.1 R1.fastq.gz", "0:24.14 1:0", "A:79804780;C:59210742;G:62058843;T:75829949;N:24", 24, 0, null, null, 79804780, 59210742, 62058843, 75829949, 24, "SRX3058686", "SRS2404541", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.68237, null, 0.04834, null, 0.76641, null, 0.51471, 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"], [43193, "SRR5893160", "SRX3058685", "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", "AG01428.2", "AG01428.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01428.2_R1.fastq.gz", "fastq", 224388938.0, 9254703.0, "AG01428.2 R1.fastq.gz", "0:24.25 1:0", "A:65443504;C:47487095;G:49760378;T:61697961;N:0", 24, 0, null, null, 65443504, 47487095, 49760378, 61697961, 0, "SRX3058685", "SRS2404541", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.68875, null, 0.05379, null, 0.76428, null, 0.51331, 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"], [43461, "SRR5947670", "SRX3106441", "SRS2441704", "SRP115809", "PRJNA399156", "Best practices for genome wide RNA structure analysis: combination of mutational profiles and drop off information", "PRJNA399156", "Other", "Genome wide RNA structure maps have recently become available through the coupling of in vivo chemical probing reagents with next generation sequencing. Initial analyses relied on the identification of truncated reverse transcription reads to identify the chemically modified nucleotides but recent studies have shown that mutational signatures can also be used. While these two methods have been employed interchangeably here we show that they actually provide complementary information. Consequently analyses using exclusively one of the two methodologies may disregard a significant portion of the structural information. We find that the identity and sequence environment of the modified nucleotide greatly affects the odds of introducing a mismatch or causing reverse transcriptase drop off. Finally we identify specific mismatch signatures generated by dimethyl sulfate probing that can be used to remove false positives typically produced in RNA structurome analyses and how these signatures vary depending on the reverse transcription enzyme used.", null, null, null, "Structure seq WT 64c DMScontrol SSIII", "sseq diff rt AG01156", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:water in vivo|molecule:RNA|selection:pA|condition:control|replicate group:1|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Structure seq WT 64c DMScontrol SSIII", "AG01156.1", "AG01156.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP115809", null, null, "AG01156.1_R1.fastq.gz", "fastq", 517100428.0, 6803953.0, "AG01156.1 R1.fastq.gz", "0:76", "A:160974859;C:115062946;G:115496047;T:125549963;N:16613", 76, null, null, null, 160974859, 115062946, 115496047, 125549963, 16613, "SRX3106441", "SRS2441704", "SRA600818", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.90199, null, 0.03108, null, 0.76347, null, 0.59205, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-08-23", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43462, "SRR5947671", "SRX3106440", "SRS2441703", "SRP115809", "PRJNA399156", "Best practices for genome wide RNA structure analysis: combination of mutational profiles and drop off information", "PRJNA399156", "Other", "Genome wide RNA structure maps have recently become available through the coupling of in vivo chemical probing reagents with next generation sequencing. Initial analyses relied on the identification of truncated reverse transcription reads to identify the chemically modified nucleotides but recent studies have shown that mutational signatures can also be used. While these two methods have been employed interchangeably here we show that they actually provide complementary information. Consequently analyses using exclusively one of the two methodologies may disregard a significant portion of the structural information. We find that the identity and sequence environment of the modified nucleotide greatly affects the odds of introducing a mismatch or causing reverse transcriptase drop off. Finally we identify specific mismatch signatures generated by dimethyl sulfate probing that can be used to remove false positives typically produced in RNA structurome analyses and how these signatures vary depending on the reverse transcription enzyme used.", null, null, null, "Structure seq WT 64c DMS SSIII", "sseq diff rt AG01157", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 2% in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:2|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Structure seq WT 64c DMS SSIII", "AG01157.1", "AG01157.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP115809", null, null, "AG01157.1_R1.fastq.gz", "fastq", 871489644.0, 11466969.0, "AG01157.1 R1.fastq.gz", "0:76", "A:266800542;C:191908328;G:203292331;T:209460678;N:27765", 76, null, null, null, 266800542, 191908328, 203292331, 209460678, 27765, "SRX3106440", "SRS2441703", "SRA600818", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.86928, null, 0.02591, null, 0.76648, null, 0.53487, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-08-23", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43463, "SRR5947672", "SRX3106439", "SRS2441702", "SRP115809", "PRJNA399156", "Best practices for genome wide RNA structure analysis: combination of mutational profiles and drop off information", "PRJNA399156", "Other", "Genome wide RNA structure maps have recently become available through the coupling of in vivo chemical probing reagents with next generation sequencing. Initial analyses relied on the identification of truncated reverse transcription reads to identify the chemically modified nucleotides but recent studies have shown that mutational signatures can also be used. While these two methods have been employed interchangeably here we show that they actually provide complementary information. Consequently analyses using exclusively one of the two methodologies may disregard a significant portion of the structural information. We find that the identity and sequence environment of the modified nucleotide greatly affects the odds of introducing a mismatch or causing reverse transcriptase drop off. Finally we identify specific mismatch signatures generated by dimethyl sulfate probing that can be used to remove false positives typically produced in RNA structurome analyses and how these signatures vary depending on the reverse transcription enzyme used.", null, null, null, "Structure seq WT 64c DMScontrol TGIRT", "sseq diff rt AG01158", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:water in vivo|molecule:RNA|selection:pA|condition:control|replicate group:3|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Structure seq WT 64c DMScontrol TGIRT", "AG01158.1", "AG01158.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP115809", null, null, "AG01158.1_R1.fastq.gz", "fastq", 631534236.0, 8309661.0, "AG01158.1 R1.fastq.gz", "0:76", "A:196134774;C:139009195;G:141013972;T:155355718;N:20577", 76, null, null, null, 196134774, 139009195, 141013972, 155355718, 20577, "SRX3106439", "SRS2441702", "SRA600818", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.86058, null, 0.04523, null, 0.76682, null, 0.58799, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-08-23", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43464, "SRR5947673", "SRX3106438", "SRS2441701", "SRP115809", "PRJNA399156", "Best practices for genome wide RNA structure analysis: combination of mutational profiles and drop off information", "PRJNA399156", "Other", "Genome wide RNA structure maps have recently become available through the coupling of in vivo chemical probing reagents with next generation sequencing. Initial analyses relied on the identification of truncated reverse transcription reads to identify the chemically modified nucleotides but recent studies have shown that mutational signatures can also be used. While these two methods have been employed interchangeably here we show that they actually provide complementary information. Consequently analyses using exclusively one of the two methodologies may disregard a significant portion of the structural information. We find that the identity and sequence environment of the modified nucleotide greatly affects the odds of introducing a mismatch or causing reverse transcriptase drop off. Finally we identify specific mismatch signatures generated by dimethyl sulfate probing that can be used to remove false positives typically produced in RNA structurome analyses and how these signatures vary depending on the reverse transcription enzyme used.", null, null, null, "Structure seq WT 64c DMS TGIRT", "sseq diff rt AG01159", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 2% in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:4|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Structure seq WT 64c DMS TGIRT", "AG01159.1", "AG01159.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP115809", null, null, "AG01159.1_R1.fastq.gz", "fastq", 658716700.0, 8667325.0, "AG01159.1 R1.fastq.gz", "0:76", "A:200810238;C:143643567;G:154463128;T:159778992;N:20775", 76, null, null, null, 200810238, 143643567, 154463128, 159778992, 20775, "SRX3106438", "SRS2441701", "SRA600818", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.81918, null, 0.03506, null, 0.76733, null, 0.52575, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-08-23", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [48356, "SRR5893042", "SRX3058803", "SRS2404515", "SRP149556", "PRJNA473824", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq", "PRJNA473824", "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.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse WT 64c R0 B2", "dev timecourse AG00671", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|replicate group:4|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse WT 64c R0 B2", "AG00671.2", "AG00671.2", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP149556", null, null, "AG00671.2_R1.fastq.gz AG00671.2_R2.fastq.gz", "fastq fastq", 3401007752.0, 22375051.0, "AG00671.2 R1.fastq.gz", "0:76 1:76", "A:761237295;C:934945811;G:938845233;T:765218661;N:760752", 76, 76, null, null, 761237295, 934945811, 938845233, 765218661, 760752, "SRX3058803", "SRS2404515", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.71455, 0.77271, 0.06416, 0.06853, 0.77017, 0.77189, 0.48808, 0.48936, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [48358, "SRR5893044", "SRX3058801", "SRS2404514", "SRP149556", "PRJNA473824", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq", "PRJNA473824", "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.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse WT 64c pA B1", "dev timecourse AG00644", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:1|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse WT 64c pA B1", "AG00644.1", "AG00644.1", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP149556", null, null, "AG00644.1_R1.fastq.gz AG00644.1_R2.fastq.gz", "fastq fastq", 2457941384.0, 16170667.0, "AG00644.1 R2.fastq.gz", "0:76 1:76", "A:655179090;C:570607586;G:571155579;T:658430586;N:2568543", 76, 76, null, null, 655179090, 570607586, 571155579, 658430586, 2568543, "SRX3058801", "SRS2404514", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.94406, 0.94075, 0.02483, 0.02699, 0.76936, 0.76966, 0.48505, 0.48646, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [48359, "SRR5893045", "SRX3058800", "SRS2404517", "SRP149556", "PRJNA473824", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq", "PRJNA473824", "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.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse WT 64c pA B2", "dev timecourse AG00645", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:1|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse WT 64c pA B2", "AG00645.1", "AG00645.1", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP149556", null, null, "AG00645.1_R1.fastq.gz AG00645.1_R2.fastq.gz", "fastq fastq", 2643787680.0, 17393340.0, "AG00645.1 R1.fastq.gz", "0:76 1:76", "A:704257377;C:614686679;G:614950025;T:707119985;N:2773614", 76, 76, null, null, 704257377, 614686679, 614950025, 707119985, 2773614, "SRX3058800", "SRS2404517", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.93726, 0.94194, 0.02686, 0.02578, 0.76834, 0.76893, 0.48339, 0.47898, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [48364, "SRR5893050", "SRX3058795", "SRS2404522", "SRP149556", "PRJNA473824", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq", "PRJNA473824", "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.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse WT 64c R0 B1", "dev timecourse AG00670", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|replicate group:4|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse WT 64c R0 B1", "AG00670.1", "AG00670.1", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP149556", null, null, "AG00670.1_R1.fastq.gz AG00670.1_R2.fastq.gz", "fastq fastq", 2692216248.0, 17711949.0, "AG00670.1 R1.fastq.gz", "0:76 1:76", "A:681268366;C:669533858;G:662344502;T:673374314;N:5695208", 76, 76, null, null, 681268366, 669533858, 662344502, 673374314, 5695208, "SRX3058795", "SRS2404522", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.858, 0.83961, 0.06542, 0.06545, 0.76623, 0.76463, 0.47797, 0.48023, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [48365, "SRR5893051", "SRX3058794", "SRS2404515", "SRP149556", "PRJNA473824", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq", "PRJNA473824", "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.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse WT 64c R0 B2", "dev timecourse AG00671", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|replicate group:4|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse WT 64c R0 B2", "AG00671.1", "AG00671.1", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP149556", null, null, "AG00671.1_R1.fastq.gz AG00671.1_R2.fastq.gz", "fastq fastq", 1411014176.0, 9282988.0, "AG00671.1 R2.fastq.gz", "0:76 1:76", "A:356427462;C:351288483;G:348446516;T:351946038;N:2905677", 76, 76, null, null, 356427462, 351288483, 348446516, 351946038, 2905677, "SRX3058794", "SRS2404515", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.83575, 0.85161, 0.06672, 0.06526, 0.76416, 0.76615, 0.48088, 0.47816, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [48366, "SRR5893064", "SRX3058781", "SRS2404533", "SRP149556", "PRJNA473824", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq", "PRJNA473824", "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.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse WT TinyLNA430 64c R0 B1", "dev timecourse AG00728", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:tinyLNA miR 430|molecule:RNA|selection:r0|replicate group:10|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse WT TinyLNA430 64c R0 B1", "AG00728.1", "AG00728.1", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP149556", null, null, "AG00728.1_R1.fastq.gz AG00728.1_R2.fastq.gz", "fastq fastq", 2789035232.0, 18348916.0, "AG00728.1 R1.fastq.gz", "0:76 1:76", "A:746104532;C:614735198;G:636481842;T:785596249;N:6117411", 76, 76, null, null, 746104532, 614735198, 636481842, 785596249, 6117411, "SRX3058781", "SRS2404533", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.51926, 0.49218, 0.08229, 0.0936, 0.80744, 0.8103, 0.48989, 0.48658, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [48369, "SRR5893067", "SRX3058778", "SRS2404533", "SRP149556", "PRJNA473824", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq", "PRJNA473824", "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.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse WT TinyLNA430 64c R0 B1", "dev timecourse AG00728", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:tinyLNA miR 430|molecule:RNA|selection:r0|replicate group:10|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse WT TinyLNA430 64c R0 B1", "AG00728.2", "AG00728.2", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP149556", null, null, "AG00728.2_R1.fastq.gz AG00728.2_R2.fastq.gz", "fastq fastq", 3094128568.0, 20356109.0, "AG00728.2 R2.fastq.gz", "0:76 1:76", "A:788885030;C:743206390;G:779938637;T:769114909;N:12983602", 76, 76, null, null, 788885030, 743206390, 779938637, 769114909, 12983602, "SRX3058778", "SRS2404533", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.45295, 0.45728, 0.06671, 0.06598, 0.81389, 0.81213, 0.48974, 0.48842, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [48377, "SRR5893164", "SRX3058681", "SRS2404572", "SRP149556", "PRJNA473824", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq", "PRJNA473824", "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.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse WT a Am 64c pA B1", "dev timecourse AG00692", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|replicate group:7|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse WT a Am 64c pA B1", "AG00692.1", "AG00692.1", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP149556", null, null, "AG00692.1_R1.fastq.gz AG00692.1_R2.fastq.gz", "fastq fastq", 1769692528.0, 11642714.0, "AG00692.1 R1.fastq.gz", "0:76 1:76", "A:473892393;C:411257494;G:409923797;T:473090107;N:1528737", 76, 76, null, null, 473892393, 411257494, 409923797, 473090107, 1528737, "SRX3058681", "SRS2404572", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.91805, 0.92435, 0.02685, 0.02528, 0.76903, 0.76893, 0.49124, 0.48516, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [48378, "SRR5893165", "SRX3058680", "SRS2404575", "SRP149556", "PRJNA473824", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq", "PRJNA473824", "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.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse WT a Am 64c pA B2", "dev timecourse AG00693", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|replicate group:7|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse WT a Am 64c pA B2", "AG00693.1", "AG00693.1", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP149556", null, null, "AG00693.1_R1.fastq.gz AG00693.1_R2.fastq.gz", "fastq fastq", 2431950600.0, 15999675.0, "AG00693.1 R1.fastq.gz", "0:76 1:76", "A:649992656;C:564963471;G:562148972;T:652726417;N:2119084", 76, 76, null, null, 649992656, 564963471, 562148972, 652726417, 2119084, "SRX3058680", "SRS2404575", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.92915, 0.93349, 0.02655, 0.02536, 0.76469, 0.76556, 0.48791, 0.48893, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51152, "SRR8552544", "SRX5354346", "SRS4345564", "SRP184786", "PRJNA521558", "Brd4 and p300 confer transcriptional competency during zygotic genome activation", "PRJNA521558", "Other", "The awakening of the genome post fertilization is a cornerstone of animal development. However the mechanisms that activate the silent genome post fertilization are poorly understood. Here we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.", null, null, null, "mRNA seq WT 2h R0", "mRNA seq WT 2h R0 AGN001827", null, "strain:TU/AB|age:2.0|dev stage:64 cell|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|sample ref:AGS001459|replicate ref:AGN001827|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq WT 2h R0", "AGR002489", "AGR002489", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP184786", null, null, "AGR002489_R1.fastq.gz", "fastq", 1915424276.0, 25202951.0, "AGR002489 R1.fastq.gz", "0:76", "A:427998951;C:502027263;G:488957899;T:496384297;N:55866", 76, null, null, null, 427998951, 502027263, 488957899, 496384297, 55866, "SRX5354346", "SRS4345564", "SRA847217", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.83803, null, 0.08509, null, 0.75753, null, 0.47975, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-02-08", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51174, "SRR8552566", "SRX5354324", "SRS4345542", "SRP184786", "PRJNA521558", "Brd4 and p300 confer transcriptional competency during zygotic genome activation", "PRJNA521558", "Other", "The awakening of the genome post fertilization is a cornerstone of animal development. However the mechanisms that activate the silent genome post fertilization are poorly understood. Here we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.", null, null, null, "ClickIT pulldown RNA seq ClickIT pulldown WT with chk1 treatment at 4h", "ClickIT pulldown RNA seq 4h chk1 CiT AGN001959", null, "strain:TU/AB|age:4.0|dev stage:16 cell|sex:pooled male and female|tissue:embryo|treatment:chk1|molecule:RNA|selection:click it|sample ref:AGS001555|replicate ref:AGN001959|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "ClickIT pulldown RNA seq ClickIT pulldown WT with chk1 treatment at 4h", "AGR002643", "AGR002643", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP184786", null, null, "AGR002643_R1.fastq.gz", "fastq", 687656208.0, 9048108.0, "AGR002643 R1.fastq.gz", "0:76", "A:169295405;C:170652179;G:163608326;T:184081751;N:18547", 76, null, null, null, 169295405, 170652179, 163608326, 184081751, 18547, "SRX5354324", "SRS4345542", "SRA847217", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.79745, null, 0.19948, null, 0.89514, null, 0.85947, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-12", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51177, "SRR8552569", "SRX5354321", "SRS4345539", "SRP184786", "PRJNA521558", "Brd4 and p300 confer transcriptional competency during zygotic genome activation", "PRJNA521558", "Other", "The awakening of the genome post fertilization is a cornerstone of animal development. However the mechanisms that activate the silent genome post fertilization are poorly understood. Here we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.", null, null, null, "ClickIT pulldown RNA seq ClickIT pulldown WT with chk1 and triptolide treatment at 4h", "ClickIT pulldown RNA seq 4h chk1 trip CiT AGN001960", null, "strain:TU/AB|age:4.0|dev stage:16 cell|sex:pooled male and female|tissue:embryo|treatment:chk1 triptolide|molecule:RNA|selection:click it|sample ref:AGS001556|replicate ref:AGN001960|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "ClickIT pulldown RNA seq ClickIT pulldown WT with chk1 and triptolide treatment at 4h", "AGR002644", "AGR002644", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP184786", null, null, "AGR002644_R1.fastq.gz", "fastq", 809282124.0, 10648449.0, "AGR002644 R1.fastq.gz", "0:76", "A:186796451;C:196752176;G:194442504;T:231268877;N:22116", 76, null, null, null, 186796451, 196752176, 194442504, 231268877, 22116, "SRX5354321", "SRS4345539", "SRA847217", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.8729, null, 0.13487, null, 0.91301, null, 0.89113, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-12", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51344, "SRR8784155", "SRX5574136", "SRS4536700", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.", null, null, null, "RESA WT 32c DL B2", "RESA WT 32c DL B2 AGN000462", null, "strain:TU/AB|age:2|dev stage:32 cell|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection|molecule:RNA|sample ref:AGS000442|replicate ref:AGN000462|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA WT 32c DL B2", "AGR000585", "AGR000585", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000585_R1.fastq.gz", "fastq", 5485540768.0, 72178168.0, "AGR000585 R1.fastq.gz", "0:76", "A:1615217489;C:1408248366;G:1358118728;T:1103657676;N:298509", 76, null, null, null, 1615217489, 1408248366, 1358118728, 1103657676, 298509, "SRX5574136", "SRS4536700", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.88108, null, 0.06907, null, 0.78169, null, 0.55768, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51348, "SRR8784159", "SRX5574132", "SRS4536701", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.", null, null, null, "RESA WT 32c DL B1", "RESA WT 32c DL B1 AGN000461", null, "strain:TU/AB|age:2|dev stage:32 cell|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection|molecule:RNA|sample ref:AGS000442|replicate ref:AGN000461|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA WT 32c DL B1", "AGR000582", "AGR000582", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000582_R1.fastq.gz", "fastq", 748685272.0, 9851122.0, "AGR000582 R1.fastq.gz", "0:76", "A:214891646;C:203114826;G:183446648;T:147202284;N:29868", 76, null, null, null, 214891646, 203114826, 183446648, 147202284, 29868, "SRX5574132", "SRS4536701", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.844, null, 0.0636, null, 0.78082, null, 0.5627, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51349, "SRR8784160", "SRX5574131", "SRS4536701", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.", null, null, null, "RESA WT 32c DL B1", "RESA WT 32c DL B1 AGN000461", null, "strain:TU/AB|age:2|dev stage:32 cell|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection|molecule:RNA|sample ref:AGS000442|replicate ref:AGN000461|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA WT 32c DL B1", "AGR000583", "AGR000583", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000583_R1.fastq.gz", "fastq", 399125096.0, 5251646.0, "AGR000583 R1.fastq.gz", "0:76", "A:115638559;C:109012627;G:97898553;T:76560942;N:14415", 76, null, null, null, 115638559, 109012627, 97898553, 76560942, 14415, "SRX5574131", "SRS4536701", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.86449, null, 0.06427, null, 0.7904, null, 0.56886, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51350, "SRR8784161", "SRX5574130", "SRS4536701", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.", null, null, null, "RESA WT 32c DL B1", "RESA WT 32c DL B1 AGN000461", null, "strain:TU/AB|age:2|dev stage:32 cell|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection|molecule:RNA|sample ref:AGS000442|replicate ref:AGN000461|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA WT 32c DL B1", "AGR000581", "AGR000581", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000581_R1.fastq.gz", "fastq", 4127680156.0, 54311581.0, "AGR000581 R1.fastq.gz", "0:76", "A:1203160682;C:1088713091;G:994274977;T:841153460;N:377946", 76, null, null, null, 1203160682, 1088713091, 994274977, 841153460, 377946, "SRX5574130", "SRS4536701", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.88277, null, 0.06873, null, 0.78445, null, 0.55482, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51351, "SRR8784162", "SRX5574129", "SRS4536700", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.", null, null, null, "RESA WT 32c DL B2", "RESA WT 32c DL B2 AGN000462", null, "strain:TU/AB|age:2|dev stage:32 cell|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection|molecule:RNA|sample ref:AGS000442|replicate ref:AGN000462|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA WT 32c DL B2", "AGR000584", "AGR000584", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000584_R1.fastq.gz", "fastq", 3692329356.0, 48583281.0, "AGR000584 R1.fastq.gz", "0:76", "A:1086979495;C:939332062;G:909920364;T:755758531;N:338904", 76, null, null, null, 1086979495, 939332062, 909920364, 755758531, 338904, "SRX5574129", "SRS4536700", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.87989, null, 0.06943, null, 0.78324, null, 0.5567, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51352, "SRR8784163", "SRX5574128", "SRS4536699", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.", null, null, null, "RESA WT 32c r2 B3", "RESA WT 32c r2 B3 AGN000590", null, "strain:TU/AB|age:2|dev stage:32 cell|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|sample ref:AGS000535|replicate ref:AGN000590|replicate order:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA WT 32c r2 B3", "AGR000783", "AGR000783", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000783_R1.fastq.gz AGR000783_R2.fastq.gz", "fastq fastq", 1617867480.0, 10643865.0, "AGR000783 R1.fastq.gz", "0:76 1:76", "A:487377678;C:324054887;G:324329007;T:479297973;N:2807935", 76, 76, null, null, 487377678, 324054887, 324329007, 479297973, 2807935, "SRX5574128", "SRS4536699", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.85088, 0.85003, 0.03672, 0.03663, 0.96771, 0.96822, 0.47246, 0.48068, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51357, "SRR8784168", "SRX5574123", "SRS4536695", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.", null, null, null, "RESA WT 32c r2 B1", "RESA WT 32c r2 B1 AGN000585", null, "strain:TU/AB|age:2|dev stage:32 cell|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|sample ref:AGS000535|replicate ref:AGN000585|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA WT 32c r2 B1", "AGR000780", "AGR000780", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000780_R1.fastq.gz AGR000780_R2.fastq.gz", "fastq fastq", 1681768888.0, 11064269.0, "AGR000780 R1.fastq.gz", "0:76 1:76", "A:505494052;C:337906595;G:338065121;T:497364873;N:2938247", 76, 76, null, null, 505494052, 337906595, 338065121, 497364873, 2938247, "SRX5574123", "SRS4536695", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.85285, 0.85386, 0.03748, 0.03778, 0.96779, 0.9681, 0.47501, 0.47905, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51370, "SRR8784181", "SRX5574110", "SRS4536687", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.", null, null, null, "RESA WT 32c r2 B2", "RESA WT 32c r2 B2 AGN000586", null, "strain:TU/AB|age:2|dev stage:32 cell|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|sample ref:AGS000535|replicate ref:AGN000586|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA WT 32c r2 B2", "AGR000781", "AGR000781", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000781_R1.fastq.gz AGR000781_R2.fastq.gz", "fastq fastq", 744470920.0, 4897835.0, "AGR000781 R1.fastq.gz", "0:76 1:76", "A:223413105;C:150069118;G:150396751;T:219294649;N:1297297", 76, 76, null, null, 223413105, 150069118, 150396751, 219294649, 1297297, "SRX5574110", "SRS4536687", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.84699, 0.84827, 0.03648, 0.03659, 0.96771, 0.96788, 0.4851, 0.48316, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51371, "SRR8784182", "SRX5574109", "SRS4536687", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the RESA libraries part of the study.", null, null, null, "RESA WT 32c r2 B2", "RESA WT 32c r2 B2 AGN000586", null, "strain:TU/AB|age:2|dev stage:32 cell|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|sample ref:AGS000535|replicate ref:AGN000586|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA WT 32c r2 B2", "AGR000782", "AGR000782", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000782_R1.fastq.gz AGR000782_R2.fastq.gz", "fastq fastq", 2728809336.0, 17952693.0, "AGR000782 R1.fastq.gz", "0:76 1:76", "A:820893743;C:547298890;G:549853268;T:807123376;N:3640059", 76, 76, null, null, 820893743, 547298890, 549853268, 807123376, 3640059, "SRX5574109", "SRS4536687", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.85693, 0.85768, 0.03694, 0.03654, 0.96749, 0.9681, 0.47802, 0.47988, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51615, "SRR8788626", "SRX5578497", "SRS4540274", "SRP189512", "PRJNA529241", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse", "PRJNA529241", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse WT 4c R0 B1", "Developmental timecourse WT 4c R0 B1 AGN000666", null, "strain:TU/AB|age:1.0|dev stage:4 cell|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|sample ref:AGS000585|replicate ref:AGN000666|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse WT 4c R0 B1", "AGR000861", "AGR000861", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189512", null, null, "AGR000861_R2.fastq.gz AGR000861_R1.fastq.gz", "fastq fastq", 2888554344.0, 19003647.0, "AGR000861 R1.fastq.gz", "0:76 1:76", "A:673571075;C:760569181;G:775244536;T:678822696;N:346856", 76, 76, null, null, 673571075, 760569181, 775244536, 678822696, 346856, "SRX5578497", "SRS4540274", "SRA866166", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.75836, 0.8073, 0.07453, 0.07791, 0.76566, 0.76745, 0.48548, 0.48444, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51616, "SRR8788627", "SRX5578496", "SRS4540274", "SRP189512", "PRJNA529241", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse", "PRJNA529241", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse WT 4c R0 B1", "Developmental timecourse WT 4c R0 B1 AGN000666", null, "strain:TU/AB|age:1.0|dev stage:4 cell|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|sample ref:AGS000585|replicate ref:AGN000666|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse WT 4c R0 B1", "AGR000860", "AGR000860", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189512", null, null, "AGR000860_R1.fastq.gz AGR000860_R2.fastq.gz", "fastq fastq", 1684739272.0, 11083811.0, "AGR000860 R1.fastq.gz", "0:76 1:76", "A:429432817;C:412139047;G:414231556;T:426015778;N:2920074", 76, 76, null, null, 429432817, 412139047, 414231556, 426015778, 2920074, "SRX5578496", "SRS4540274", "SRA866166", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.86855, 0.85707, 0.07231, 0.07348, 0.76187, 0.76049, 0.47575, 0.48049, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51617, "SRR8788628", "SRX5578495", "SRS4540273", "SRP189512", "PRJNA529241", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse", "PRJNA529241", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT thousands of maternal transcripts are regulated however how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay we identified cis regulatory sequences in the three prime UTR including poly U motifs that are associated with mRNA stability. In contrast miR 430 target sequences UAUUUAUU AU rich elements ARE CCUC and CUGC elements emerged as destabilizing motifs with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse WT 2c R0 B2", "Developmental timecourse WT 2c R0 B2 AGN000665", null, "strain:TU/AB|age:0.75|dev stage:2 cell|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|sample ref:AGS000584|replicate ref:AGN000665|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse WT 2c R0 B2", "AGR000859", "AGR000859", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189512", null, null, "AGR000859_R1.fastq.gz AGR000859_R2.fastq.gz", "fastq fastq", 2132978912.0, 14032756.0, "AGR000859 R1.fastq.gz", "0:76 1:76", "A:453107239;C:603446010;G:622466425;T:453479291;N:479947", 76, 76, null, null, 453107239, 603446010, 622466425, 453479291, 479947, "SRX5578495", "SRS4540273", "SRA866166", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.65481, 0.69653, 0.06284, 0.06531, 0.77256, 0.774, 0.48127, 0.47849, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 133, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation\" = :p0 and \"experiment.library_selection\" = :p1 order by rowid limit 101", "params": {"p0": "Cleavage", "p1": "unspecified"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified", "results": [{"value": "OTHER", "label": "OTHER", "count": 72, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified&experiment.library_strategy=OTHER", "selected": false}, {"value": "RNA-Seq", "label": "RNA-Seq", "count": 60, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "FL-cDNA", "label": "FL-cDNA", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified&experiment.library_strategy=FL-cDNA", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 133, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified", "results": [{"value": "unspecified", "label": "unspecified", "count": 133, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 85, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified&experiment.library_layout=SINGLE", "selected": false}, {"value": "PAIRED", "label": "PAIRED", "count": 48, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 133, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified", "results": [{"value": "Embryo", "label": "Embryo", "count": 133, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified", "results": [{"value": "Cleavage", "label": "Cleavage", "count": 133, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=unspecified", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 133, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified&tissue_curation_coarse=All+anatomical+structures", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified", "results": [{"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 132, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified&tissue_curation=Embryo+Imprecise", "selected": false}, {"value": "Whole Organism", "label": "Whole Organism", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified&tissue_curation=Whole+Organism", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified", "results": [{"value": "unknown", "label": "unknown", "count": 133, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified&technology=unknown", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": "51617", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Cleavage&experiment.library_selection=unspecified&_next=51617", "private": false, "allow_execute_sql": true, "query_ms": 86.19501599605428}