{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_selection = \"unspecified\" and tissue_curation_coarse = \"All anatomical structures\"", "rows": [[36581, "SRR594769", "SRX195432", "SRS369361", "SRP016134", "PRJNA177654", "Danio rerio Transcriptome or Gene expression", "PRJNA177654", "Other", "We use zebrafish embryos to characterise the transcriptome of the developing blood and endothelium.", null, null, "1", "Test", "GFP Negative 1", null, null, null, null, null, null, null, null, null, null, "Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development", "Embryos", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP016134", null, null, null, null, 2525199228.0, 65962848.0, "GFP Positive", "0:38.28", "A:665802914;C:594493287;G:612298433;T:652078696;N:525898", 38, null, null, null, 665802914, 594493287, 612298433, 652078696, 525898, "SRX195432", "SRS369361", null, null, "University of Cambridge", 1, 0.89062, null, 0.09595, null, 0.74059, null, 0.47506, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-07-22", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36582, "SRR594771", "SRX195432", "SRS369361", "SRP016134", "PRJNA177654", "Danio rerio Transcriptome or Gene expression", "PRJNA177654", "Other", "We use zebrafish embryos to characterise the transcriptome of the developing blood and endothelium.", null, null, "1", "Test", "GFP Negative 1", null, null, null, null, null, null, null, null, null, null, "Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development", "Embryos", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP016134", null, null, "gfp_negative_replicate_1_sequence.txt.gz", "fastq", 2549682148.0, 66546682.0, "GFP Negative", "0:38.31", "A:686329592;C:587342682;G:601330559;T:674194074;N:485241", 38, null, null, null, 686329592, 587342682, 601330559, 674194074, 485241, "SRX195432", "SRS369361", null, null, "University of Cambridge", 1, 0.90413, null, 0.13272, null, 0.71342, null, 0.48186, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-07-22", "Undetermined", "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"], [39687, "SRR2051113", "SRX1048368", "SRS952733", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P39", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 3.0 uM CPO Rep 4", "P39", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP059060", null, null, "P39_EL4517_GATCAG_L001_R1_001.fastq.gz P39_EL4517_GATCAG_L002_R1_001.fastq.gz P39_EL4517_GATCAG_L007_R1_001.fastq.gz P39_EL4517_GATCAG_L008_R1_001.fastq.gz", "fastq fastq fastq fastq", 4090297192.0, 40497992.0, "P39", "0:101", "A:1016157993;C:993771683;G:965986507;T:1113686588;N:694421", 101, null, null, null, 1016157993, 993771683, 965986507, 1113686588, 694421, "SRX1048368", "SRS952733", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.9417, null, 0.14428, null, 0.68937, null, 0.5438, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39688, "SRR2051110", "SRX1048367", "SRS952731", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P37", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 3.0 uM CPO Rep 3", "P37", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP059060", null, null, "P37_EL4516_ACTTGA_L008_R1_001.fastq.gz P37_EL4516_ACTTGA_L007_R1_001.fastq.gz P37_EL4516_ACTTGA_L002_R1_001.fastq.gz P37_EL4516_ACTTGA_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4647442886.0, 46014286.0, "P37", "0:101", "A:1149955739;C:1129088798;G:1093234722;T:1274375148;N:788479", 101, null, null, null, 1149955739, 1129088798, 1093234722, 1274375148, 788479, "SRX1048367", "SRS952731", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94585, null, 0.12571, null, 0.68633, null, 0.52597, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39689, "SRR2051112", "SRX1048366", "SRS952732", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P36", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 3.0 uM CPO Rep 2", "P36", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP059060", null, null, "P36_EL4527_CCGTCC_L008_R1_001.fastq.gz P36_EL4527_CCGTCC_L007_R1_001.fastq.gz P36_EL4527_CCGTCC_L002_R1_001.fastq.gz P36_EL4527_CCGTCC_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4296894611.0, 42543511.0, "P36", "0:101", "A:1050039699;C:1061123166;G:1022913715;T:1162094624;N:723407", 101, null, null, null, 1050039699, 1061123166, 1022913715, 1162094624, 723407, "SRX1048366", "SRS952732", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94977, null, 0.13188, null, 0.70976, null, 0.52728, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39690, "SRR2051109", "SRX1048365", "SRS952730", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P35", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 3.0 uM CPO Rep 1", "P35", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP059060", null, null, "P35_EL4526_ATGTCA_L008_R1_001.fastq.gz P35_EL4526_ATGTCA_L007_R1_001.fastq.gz P35_EL4526_ATGTCA_L002_R1_001.fastq.gz P35_EL4526_ATGTCA_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4094752706.0, 40542106.0, "P35", "0:101", "A:1009779802;C:1004374749;G:969241794;T:1110655194;N:701167", 101, null, null, null, 1009779802, 1004374749, 969241794, 1110655194, 701167, "SRX1048365", "SRS952730", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94442, null, 0.13203, null, 0.70023, null, 0.53953, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39691, "SRR2051102", "SRX1048364", "SRS952729", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P29", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 1.0 uM CPO Rep 4", "P29", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP059060", null, null, "P29_EL4510_CTTGTA_L008_R1_001.fastq.gz P29_EL4510_CTTGTA_L007_R1_001.fastq.gz P29_EL4510_CTTGTA_L002_R1_001.fastq.gz P29_EL4510_CTTGTA_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4983571896.0, 49342296.0, "P29", "0:101", "A:1247122516;C:1202173111;G:1173654831;T:1359775597;N:845841", 101, null, null, null, 1247122516, 1202173111, 1173654831, 1359775597, 845841, "SRX1048364", "SRS952729", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94329, null, 0.13234, null, 0.68286, null, 0.51586, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39692, "SRR2051100", "SRX1048363", "SRS952727", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P28", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 1.0 uM CPO Rep 3", "P28", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP059060", null, null, "P28_EL4509_CAGATC_L008_R1_001.fastq.gz P28_EL4509_CAGATC_L007_R1_001.fastq.gz P28_EL4509_CAGATC_L002_R1_001.fastq.gz P28_EL4509_CAGATC_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4032678914.0, 39927514.0, "P28", "0:101", "A:1015356577;C:970369004;G:937306142;T:1108957703;N:689488", 101, null, null, null, 1015356577, 970369004, 937306142, 1108957703, 689488, "SRX1048363", "SRS952727", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.93887, null, 0.13869, null, 0.69079, null, 0.52237, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39693, "SRR2051101", "SRX1048362", "SRS952728", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P26", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 1.0 uM CPO Rep 2", "P26", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP059060", null, null, "P26_EL4508_GCCAAT_L001_R1_001.fastq.gz P26_EL4508_GCCAAT_L007_R1_001.fastq.gz P26_EL4508_GCCAAT_L008_R1_001.fastq.gz P26_EL4508_GCCAAT_L002_R1_001.fastq.gz", "fastq fastq fastq fastq", 6526758875.0, 64621375.0, "P26", "0:101", "A:1635664768;C:1568967965;G:1518148006;T:1802863908;N:1114228", 101, null, null, null, 1635664768, 1568967965, 1518148006, 1802863908, 1114228, "SRX1048362", "SRS952728", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.93822, null, 0.15203, null, 0.68609, null, 0.53171, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39694, "SRR2051096", "SRX1048361", "SRS952726", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P25", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 1.0 uM CPO Rep 1", "P25", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP059060", null, null, "P25_EL4511_ATCACG_L001_R1_001.fastq.gz P25_EL4511_ATCACG_L002_R1_001.fastq.gz P25_EL4511_ATCACG_L007_R1_001.fastq.gz P25_EL4511_ATCACG_L008_R1_001.fastq.gz", "fastq fastq fastq fastq", 4185957322.0, 41445122.0, "P25", "0:101", "A:1081936223;C:978799105;G:956795307;T:1167714259;N:712428", 101, null, null, null, 1081936223, 978799105, 956795307, 1167714259, 712428, "SRX1048361", "SRS952726", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.9288, null, 0.17032, null, 0.6801, null, 0.51298, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39695, "SRR2051095", "SRX1048360", "SRS952725", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P19", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 0.1 uM CPO Rep 4", "P19", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP059060", null, null, "P19_EL4521_GGCTAC_L008_R1_001.fastq.gz P19_EL4521_GGCTAC_L007_R1_001.fastq.gz P19_EL4521_GGCTAC_L002_R1_001.fastq.gz P19_EL4521_GGCTAC_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4293546461.0, 42510361.0, "P19", "0:101", "A:1062707728;C:1045602693;G:1011860446;T:1172670772;N:704822", 101, null, null, null, 1062707728, 1045602693, 1011860446, 1172670772, 704822, "SRX1048360", "SRS952725", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94381, null, 0.13697, null, 0.69051, null, 0.51415, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39696, "SRR2051094", "SRX1048359", "SRS952724", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P18", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 0.1 uM CPO Rep 3", "P18", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP059060", null, null, "P18_EL4520_TAGCTT_L008_R1_001.fastq.gz P18_EL4520_TAGCTT_L007_R1_001.fastq.gz P18_EL4520_TAGCTT_L002_R1_001.fastq.gz P18_EL4520_TAGCTT_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4257944163.0, 42157863.0, "P18", "0:101", "A:1044532409;C:1049992329;G:1010166097;T:1152524203;N:729125", 101, null, null, null, 1044532409, 1049992329, 1010166097, 1152524203, 729125, "SRX1048359", "SRS952724", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94262, null, 0.14592, null, 0.69014, null, 0.52498, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39697, "SRR2051093", "SRX1048358", "SRS952723", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P17", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 0.1 uM CPO Rep 2", "P17", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP059060", null, null, "P17_EL4522_AGTCAA_L007_R1_001.fastq.gz P17_EL4522_AGTCAA_L008_R1_001.fastq.gz P17_EL4522_AGTCAA_L002_R1_001.fastq.gz P17_EL4522_AGTCAA_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4278385553.0, 42360253.0, "P17", "0:101", "A:1040955882;C:1060023973;G:1019487833;T:1157186726;N:731139", 101, null, null, null, 1040955882, 1060023973, 1019487833, 1157186726, 731139, "SRX1048358", "SRS952723", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94697, null, 0.14458, null, 0.69643, null, 0.53451, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39698, "SRR2051092", "SRX1048357", "SRS952722", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P15", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:mild phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 0.1 uM CPO Rep 1", "P15", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP059060", null, null, "P15_EL4523_AGTTCC_L001_R1_001.fastq.gz P15_EL4523_AGTTCC_L002_R1_001.fastq.gz P15_EL4523_AGTTCC_L007_R1_001.fastq.gz P15_EL4523_AGTTCC_L008_R1_001.fastq.gz", "fastq fastq fastq fastq", 4341747499.0, 42987599.0, "P15", "0:101", "A:1052621077;C:1088380866;G:1041958433;T:1158051746;N:735377", 101, null, null, null, 1052621077, 1088380866, 1041958433, 1158051746, 735377, "SRX1048357", "SRS952722", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94563, null, 0.153, null, 0.69822, null, 0.54133, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39699, "SRR2051091", "SRX1048356", "SRS952721", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "CN9", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP Control Rep 4", "CN9", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP059060", null, null, "CN9_EL4515_TTAGGC_L001_R1_001.fastq.gz CN9_EL4515_TTAGGC_L002_R1_001.fastq.gz CN9_EL4515_TTAGGC_L007_R1_001.fastq.gz CN9_EL4515_TTAGGC_L008_R1_001.fastq.gz", "fastq fastq fastq fastq", 4220387212.0, 41786012.0, "CN9", "0:101", "A:1031722430;C:1044497851;G:1005706674;T:1137783022;N:677235", 101, null, null, null, 1031722430, 1044497851, 1005706674, 1137783022, 677235, "SRX1048356", "SRS952721", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.95231, null, 0.14084, null, 0.69682, null, 0.52966, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39700, "SRR2051090", "SRX1048354", "SRS952719", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "CN8", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP Control Rep 3", "CN8", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP059060", null, null, "CN8_EL4505_CGATGT_L008_R1_001.fastq.gz CN8_EL4505_CGATGT_L007_R1_001.fastq.gz CN8_EL4505_CGATGT_L002_R1_001.fastq.gz CN8_EL4505_CGATGT_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 5835502553.0, 57777253.0, "CN8", "0:101", "A:1424369529;C:1441755207;G:1391851806;T:1576540272;N:985739", 101, null, null, null, 1424369529, 1441755207, 1391851806, 1576540272, 985739, "SRX1048354", "SRS952719", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94643, null, 0.12925, null, 0.70725, null, 0.52949, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39701, "SRR2050894", "SRX1048353", "SRS952718", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "CN7", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP Control Rep 2", "CN7", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP059060", null, null, "CN7_EL4507_ACAGTG_L008_R1_001.fastq.gz CN7_EL4507_ACAGTG_L007_R1_001.fastq.gz CN7_EL4507_ACAGTG_L002_R1_001.fastq.gz CN7_EL4507_ACAGTG_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4789094477.0, 47416777.0, "CN7", "0:101", "A:1160528098;C:1197558725;G:1155573375;T:1274638263;N:796016", 101, null, null, null, 1160528098, 1197558725, 1155573375, 1274638263, 796016, "SRX1048353", "SRS952718", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.9501, null, 0.14828, null, 0.69966, null, 0.52764, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39702, "SRR2050892", "SRX1048352", "SRS952717", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "CN5", null, "breed:wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP Control Rep 1", "CN5", "CN5 EL4506 TGACCA", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP059060", null, null, "CN5_EL4506_TGACCA_L001_R1_001.fastq.gz CN5_EL4506_TGACCA_L002_R1_001.fastq.gz CN5_EL4506_TGACCA_L007_R1_001.fastq.gz CN5_EL4506_TGACCA_L008_R1_001.fastq.gz", "fastq fastq fastq fastq", 4526144512.0, 44813312.0, "CN5", "0:101", "A:1109966549;C:1116619353;G:1075422479;T:1223366972;N:769159", 101, null, null, null, 1109966549, 1116619353, 1075422479, 1223366972, 769159, "SRX1048352", "SRS952717", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94604, null, 0.14084, null, 0.69004, null, 0.53407, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [43058, "SRR8354695", "SRX5165478", "SRS4174524", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS seq   RNA structure positive controls in vitro replicate 1", "DMS seq   RNA positives ctrl in vitro B1 AG01489", null, "strain:TU/AB|age:3.7|dev stage:oblong|sex:pooled male and female|tissue:embryo|treatment:0.5% DMS for 10 min in vitro|molecule:RNA|condition:invitro DMS|replicate group:1|replicate:1|barcode:TCTC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS seq   RNA structure positive controls in vitro replicate 1", "AG01489.1", "AG01489.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01489.1_R1.fastq.gz", "fastq", 75703530.0, 2718404.0, "AG01489.1 R1.fastq.gz", "0:27.85 1:0", "A:18206335;C:19464567;G:21319876;T:16712584;N:168", 27, 0, null, null, 18206335, 19464567, 21319876, 16712584, 168, "SRX5165478", "SRS4174524", "SRA825010", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.02389, null, 0.00591, null, 0.97654, null, 0.4758, null, 25, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-12-19", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43059, "SRR8354696", "SRX5165477", "SRS4174523", "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   RNA structure positive controls in vitro replicate 2", "DMS seq   RNA positives ctrl in vitro B2 AG01490", null, "strain:TU/AB|age:3.7|dev stage:oblong|sex:pooled male and female|tissue:embryo|treatment:0.5% DMS for 10 min in vitro|molecule:RNA|condition:invitro DMS|replicate group:1|replicate:2|barcode:GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS seq   RNA structure positive controls in vitro replicate 2", "AG01490.1", "AG01490.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01490.1_R1.fastq.gz", "fastq", 295051199.0, 10869746.0, "AG01490.1 R1.fastq.gz", "0:27.14 1:0", "A:71900468;C:76519029;G:81589099;T:65042019;N:584", 27, 0, null, null, 71900468, 76519029, 81589099, 65042019, 584, "SRX5165477", "SRS4174523", "SRA825010", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.02362, null, 0.00528, null, 0.98173, null, 0.35096, null, 19, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-12-19", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43060, "SRR8354697", "SRX5165476", "SRS4174522", "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   RNA structure positive controls in vitro replicate 1;DMS seq   RNA structure positive controls in vitro replicate 2", "Raw multiplex: DMS seq   RNA positives ctrl in vitro B1 AG01489;DMS seq   RNA positives ctrl in vitro B2 AG01490", null, "strain:TU/AB|age:3.7|dev stage:oblong|sex:pooled male and female|tissue:embryo|treatment:0.5% DMS for 10 min in vitro|molecule:RNA|condition:invitro DMS|replicate group:1|replicate:1;2|barcode:TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS seq   RNA structure positive controls in vitro replicate 1;DMS seq   RNA structure positive controls in vitro replicate 2", "AG01489.1;AG01490.1", "AG01489.1;AG01490.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MYYANXX_JBDX127_009_R1.fastq.gz", "fastq", 1115150128.0, 14673028.0, "C7MYYANXX JBDX127 009 R1.fastq.gz", "0:76", "A:313482382;C:276309346;G:291633361;T:233659719;N:65320", 76, null, null, null, 313482382, 276309346, 291633361, 233659719, 65320, "SRX5165476", "SRS4174522", "SRA825010", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00546, null, 0.00047, null, 0.98602, null, 0.51535, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-12-19", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43061, "SRR7264565", "SRX4168732", "SRS3380685", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated", null, "strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "AG01046.2;AG01047.2;AG01049.2;unrelated", "AG01046.2;AG01047.2;AG01049.2;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA22NADXX_JBBS71_021_R1.fastq.gz", "fastq", 493969676.0, 6499601.0, "HA22NADXX JBBS71 021 R1.fastq.gz", "0:76", "A:149523181;C:122615352;G:117180131;T:97949905;N:6701107", 76, null, null, null, 149523181, 122615352, 117180131, 97949905, 6701107, "SRX4168732", "SRS3380685", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43062, "SRR7264566", "SRX4168731", "SRS3380685", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated", null, "strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "AG01046.1;AG01047.1;AG01049.1;unrelated", "AG01046.1;AG01047.1;AG01049.1;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA1YWADXX_JBBS71_021_R1.fastq.gz", "fastq", 1444702012.0, 19009237.0, "HA1YWADXX JBBS71 021 R1.fastq.gz", "0:76", "A:442549747;C:365473385;G:344546726;T:292070542;N:61612", 76, null, null, null, 442549747, 365473385, 344546726, 292070542, 61612, "SRX4168731", "SRS3380685", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43063, "SRR7264567", "SRX4168730", "SRS3380690", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated", null, "strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "AG01042.6;AG01043.6;AG01044.6;unrelated", "AG01042.6;AG01043.6;AG01044.6;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HBCAFADXX_JBBR70_020_R1.fastq.gz", "fastq", 3562176468.0, 46870743.0, "HBCAFADXX JBBR70 020 R1.fastq.gz", "0:76", "A:1097921080;C:906895047;G:849908073;T:707369464;N:82804", 76, null, null, null, 1097921080, 906895047, 849908073, 707369464, 82804, "SRX4168730", "SRS3380690", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43064, "SRR7264568", "SRX4168729", "SRS3380690", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated", null, "strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "AG01042.5;AG01043.5;AG01044.5;unrelated", "AG01042.5;AG01043.5;AG01044.5;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "C562AACXX_JBBR70_NOBCX_R1.fastq.gz", "fastq", 13352386192.0, 175689292.0, "C562AACXX JBBR70 NOBCX R1.fastq.gz", "0:76", "A:4126007145;C:3372127203;G:3172182791;T:2661287884;N:20781169", 76, null, null, null, 4126007145, 3372127203, 3172182791, 2661287884, 20781169, "SRX4168729", "SRS3380690", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43065, "SRR7264569", "SRX4168728", "SRS3380690", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated", null, "strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "AG01042.4;AG01043.4;AG01044.4;unrelated", "AG01042.4;AG01043.4;AG01044.4;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA2H1ADXX_JBBR70_NOBCX_R1.fastq.gz", "fastq", 9139389880.0, 120255130.0, "HA2H1ADXX JBBR70 NOBCX R1.fastq.gz", "0:76", "A:2815354570;C:2322972018;G:2180978488;T:1817457488;N:2627316", 76, null, null, null, 2815354570, 2322972018, 2180978488, 1817457488, 2627316, "SRX4168728", "SRS3380690", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43066, "SRR7264570", "SRX4168727", "SRS3380690", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated", null, "strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "AG01042.3;AG01043.3;AG01044.3;unrelated", "AG01042.3;AG01043.3;AG01044.3;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA1YVADXX_JBBR70_NOBCX_R1.fastq.gz", "fastq", 7892000132.0, 103842107.0, "HA1YVADXX JBBR70 NOBCX R1.fastq.gz", "0:76", "A:2428266964;C:2007082407;G:1885147455;T:1568726692;N:2776614", 76, null, null, null, 2428266964, 2007082407, 1885147455, 1568726692, 2776614, "SRX4168727", "SRS3380690", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43067, "SRR7264571", "SRX4168726", "SRS3380690", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated", null, "strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "AG01042.2;AG01043.2;AG01044.2;unrelated", "AG01042.2;AG01043.2;AG01044.2;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA22NADXX_JBBR70_020_R1.fastq.gz", "fastq", 554569568.0, 7296968.0, "HA22NADXX JBBR70 020 R1.fastq.gz", "0:76", "A:168630291;C:138451887;G:131779810;T:108186590;N:7520990", 76, null, null, null, 168630291, 138451887, 131779810, 108186590, 7520990, "SRX4168726", "SRS3380690", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43068, "SRR7264572", "SRX4168725", "SRS3380690", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated", null, "strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "AG01042.1;AG01043.1;AG01044.1;unrelated", "AG01042.1;AG01043.1;AG01044.1;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA1YWADXX_JBBR70_020_R1.fastq.gz", "fastq", 1565371316.0, 20596991.0, "HA1YWADXX JBBR70 020 R1.fastq.gz", "0:76", "A:481887814;C:398331513;G:374271346;T:310815367;N:65276", 76, null, null, null, 481887814, 398331513, 374271346, 310815367, 65276, "SRX4168725", "SRS3380690", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43069, "SRR7264573", "SRX4168724", "SRS3380685", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated", null, "strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "AG01046.4;AG01047.4;AG01049.4;unrelated", "AG01046.4;AG01047.4;AG01049.4;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA2H1ADXX_JBBS71_NOBCX_R1.fastq.gz", "fastq", 8845878184.0, 116393134.0, "HA2H1ADXX JBBS71 NOBCX R1.fastq.gz", "0:76", "A:2711637569;C:2235324807;G:2105535243;T:1791610098;N:1770467", 76, null, null, null, 2711637569, 2235324807, 2105535243, 1791610098, 1770467, "SRX4168724", "SRS3380685", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43070, "SRR7264574", "SRX4168723", "SRS3380685", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated", null, "strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "AG01046.3;AG01047.3;AG01049.3;unrelated", "AG01046.3;AG01047.3;AG01049.3;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA1YVADXX_JBBS71_NOBCX_R1.fastq.gz", "fastq", 7768733452.0, 102220177.0, "HA1YVADXX JBBS71 NOBCX R1.fastq.gz", "0:76", "A:2378019627;C:1963788516;G:1851111018;T:1572409542;N:3404749", 76, null, null, null, 2378019627, 1963788516, 1851111018, 1572409542, 3404749, "SRX4168723", "SRS3380685", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 1e-05, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43071, "SRR7264575", "SRX4168722", "SRS3380686", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2", "Raw multiplex: dmsseq AG01273;dmsseq AG01274", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2", "AG01273.4;AG01274.4", "AG01273.4;AG01274.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HWKVWADXX_JBCZ103_023_R1.fastq.gz", "fastq", 7514617040.0, 98876540.0, "HWKVWADXX JBCZ103 023 R1.fastq.gz", "0:76", "A:2401597632;C:1861527917;G:1834777254;T:1415956870;N:757367", 76, null, null, null, 2401597632, 1861527917, 1834777254, 1415956870, 757367, "SRX4168722", "SRS3380686", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43072, "SRR7264576", "SRX4168721", "SRS3380689", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: RPF patA   WT 64c RPF B1;RPF patA   WT 64c RPF B2", "Raw multiplex: ribo seq pata AG01409;ribo seq pata AG01410", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:cyclohex|molecule:RNA|condition:RPF 28nt|replicate group:19|replicate:1;2|barcode:CACA;TCTC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: RPF patA   WT 64c RPF B1;RPF patA   WT 64c RPF B2", "AG01409.1;AG01410.1", "AG01409.1;AG01410.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MPPANXX_JBDL115_014_R1.fastq.gz", "fastq", 4944760108.0, 65062633.0, "C7MPPANXX JBDL115 014 R1.fastq.gz", "0:76", "A:1280812305;C:1385761238;G:1441128504;T:836702863;N:355198", 76, null, null, null, 1280812305, 1385761238, 1441128504, 836702863, 355198, "SRX4168721", "SRS3380689", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43073, "SRR7264577", "SRX4168720", "SRS3380688", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: RPF patA   WT 64c PatA RPF B1;RPF patA   WT 64c PatA RPF B2", "Raw multiplex: ribo seq pata AG01411;ribo seq pata AG01412", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:cyclohex PatA|molecule:RNA|condition:RPF 28nt|replicate group:20|replicate:1;2|barcode:CACA;TCTC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: RPF patA   WT 64c PatA RPF B1;RPF patA   WT 64c PatA RPF B2", "AG01411.1;AG01412.1", "AG01411.1;AG01412.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MPPANXX_JBDM116_015_R1.fastq.gz", "fastq", 10995071544.0, 144671994.0, "C7MPPANXX JBDM116 015 R1.fastq.gz", "0:76", "A:2850888928;C:3075001734;G:3215965099;T:1852417694;N:798089", 76, null, null, null, 2850888928, 3075001734, 3215965099, 1852417694, 798089, "SRX4168720", "SRS3380688", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43074, "SRR7264578", "SRX4168719", "SRS3380687", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2", "Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2", "AG01426.1;AG01427.1", "AG01426.1;AG01427.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MPPANXX_JBDF109_027_R1.fastq.gz", "fastq", 446991948.0, 5881473.0, "C7MPPANXX JBDF109 027 R1.fastq.gz", "0:76", "A:146192524;C:109441919;G:103882304;T:87445288;N:29913", 76, null, null, null, 146192524, 109441919, 103882304, 87445288, 29913, "SRX4168719", "SRS3380687", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 2e-05, null, 1e-05, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43075, "SRR7264579", "SRX4168718", "SRS3380687", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2", "Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2", "AG01426.2;AG01427.2", "AG01426.2;AG01427.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJC2ADXX_JBDF109_027_R1.fastq.gz", "fastq", 447485492.0, 5887967.0, "HVJC2ADXX JBDF109 027 R1.fastq.gz", "0:76", "A:146683880;C:109166579;G:104154702;T:87473352;N:6979", 76, null, null, null, 146683880, 109166579, 104154702, 87473352, 6979, "SRX4168718", "SRS3380687", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0023, null, 0.00034, null, 0.99326, null, 0.57567, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43076, "SRR7264580", "SRX4168717", "SRS3380687", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2", "Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2", "AG01426.3;AG01427.3", "AG01426.3;AG01427.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJ2TADXX_JBDF109_027_R1.fastq.gz", "fastq", 4740289176.0, 62372226.0, "HVJ2TADXX JBDF109 027 R1.fastq.gz", "0:76", "A:1552060471;C:1156267615;G:1104246757;T:927209997;N:504336", 76, null, null, null, 1552060471, 1156267615, 1104246757, 927209997, 504336, "SRX4168717", "SRS3380687", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00235, null, 0.00026, null, 0.99379, null, 0.60051, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43077, "SRR7264581", "SRX4168716", "SRS3380687", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2", "Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2", "AG01426.4;AG01427.4", "AG01426.4;AG01427.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HJTYNBCXX_JBDF109_NOBCX_R1.fastq.gz", "fastq", 6776423036.0, 89163461.0, "HJTYNBCXX JBDF109 NOBCX R1.fastq.gz", "0:76", "A:2212424663;C:1653496002;G:1573846163;T:1336100302;N:555906", 76, null, null, null, 2212424663, 1653496002, 1573846163, 1336100302, 555906, "SRX4168716", "SRS3380687", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 3e-05, null, 2e-05, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43078, "SRR7264582", "SRX4168715", "SRS3380683", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "AG01428.1;AG01429.1", "AG01428.1;AG01429.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MPPANXX_JBDG110_013_R1.fastq.gz", "fastq", 1593732388.0, 20970163.0, "C7MPPANXX JBDG110 013 R1.fastq.gz", "0:76", "A:517196379;C:393268952;G:372639155;T:310521534;N:106368", 76, null, null, null, 517196379, 393268952, 372639155, 310521534, 106368, "SRX4168715", "SRS3380683", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 2e-05, null, 0.0, null, 0.99997, null, 1.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43079, "SRR7264583", "SRX4168714", "SRS3380683", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "AG01428.2;AG01429.2", "AG01428.2;AG01429.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJC2ADXX_JBDG110_013_R1.fastq.gz", "fastq", 1268326988.0, 16688513.0, "HVJC2ADXX JBDG110 013 R1.fastq.gz", "0:76", "A:411772190;C:312434121;G:297408612;T:246654231;N:57834", 76, null, null, null, 411772190, 312434121, 297408612, 246654231, 57834, "SRX4168714", "SRS3380683", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 1e-05, null, 0.0, null, 0.99997, null, 0.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43080, "SRR7264584", "SRX4168713", "SRS3380683", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "AG01428.3;AG01429.3", "AG01428.3;AG01429.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJ2TADXX_JBDG110_013_R1.fastq.gz", "fastq", 1149592188.0, 15126213.0, "HVJ2TADXX JBDG110 013 R1.fastq.gz", "0:76", "A:373090462;C:283151050;G:269811169;T:223419849;N:119658", 76, null, null, null, 373090462, 283151050, 269811169, 223419849, 119658, "SRX4168713", "SRS3380683", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00222, null, 0.0002, null, 0.99362, null, 0.55643, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43081, "SRR7264585", "SRX4168712", "SRS3380686", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2", "Raw multiplex: dmsseq AG01273;dmsseq AG01274", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2", "AG01273.3;AG01274.3", "AG01273.3;AG01274.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJ7NADXX_JBCZ103_023_R1.fastq.gz", "fastq", 882016024.0, 11605474.0, "HVJ7NADXX JBCZ103 023 R1.fastq.gz", "0:76", "A:278837606;C:213606139;G:214029888;T:175477675;N:64716", 76, null, null, null, 278837606, 213606139, 214029888, 175477675, 64716, "SRX4168712", "SRS3380686", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 6e-05, null, 4e-05, null, 0.99995, null, 1.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43082, "SRR7264586", "SRX4168711", "SRS3380686", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2", "Raw multiplex: dmsseq AG01273;dmsseq AG01274", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2", "AG01273.2;AG01274.2", "AG01273.2;AG01274.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVK53ADXX_JBCZ103_023_R1.fastq.gz", "fastq", 2614864056.0, 34406106.0, "HVK53ADXX JBCZ103 023 R1.fastq.gz", "0:76", "A:832670351;C:647746556;G:639758530;T:494461931;N:226688", 76, null, null, null, 832670351, 647746556, 639758530, 494461931, 226688, "SRX4168711", "SRS3380686", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 5e-05, null, 2e-05, null, 0.99993, null, 0.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43083, "SRR7264587", "SRX4168710", "SRS3380684", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "AG01269.4;AG01270.4", "AG01269.4;AG01270.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MYYANXX_JBCX101_016_R1.fastq.gz", "fastq", 3504515800.0, 46112050.0, "C7MYYANXX JBCX101 016 R1.fastq.gz", "0:76", "A:1100987855;C:897481291;G:850509260;T:655386223;N:151171", 76, null, null, null, 1100987855, 897481291, 850509260, 655386223, 151171, "SRX4168710", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00251, null, 0.00024, null, 0.99334, null, 0.49363, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43084, "SRR7264588", "SRX4168709", "SRS3380684", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "AG01269.3;AG01270.3", "AG01269.3;AG01270.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJ7NADXX_JBCX101_016_R1.fastq.gz", "fastq", 1533760484.0, 20181059.0, "HVJ7NADXX JBCX101 016 R1.fastq.gz", "0:76", "A:486730101;C:387546602;G:372319444;T:287072948;N:91389", 76, null, null, null, 486730101, 387546602, 372319444, 287072948, 91389, "SRX4168709", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 4e-05, null, 2e-05, null, 0.99997, null, 1.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43085, "SRR7264589", "SRX4168708", "SRS3380686", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2", "Raw multiplex: dmsseq AG01273;dmsseq AG01274", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2", "AG01273.1;AG01274.1", "AG01273.1;AG01274.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HMHGVADXX_JBCZ103_023_R1.fastq.gz", "fastq", 2819768568.0, 37102218.0, "HMHGVADXX JBCZ103 023 R1.fastq.gz", "0:76", "A:900945260;C:699348182;G:689446355;T:529699985;N:328786", 76, null, null, null, 900945260, 699348182, 689446355, 529699985, 328786, "SRX4168708", "SRS3380686", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43086, "SRR7264590", "SRX4168707", "SRS3380684", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "AG01269.5;AG01270.5", "AG01269.5;AG01270.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MWLANXX_JBCX101_016_R1.fastq.gz", "fastq", 11187105076.0, 147198751.0, "C7MWLANXX JBCX101 016 R1.fastq.gz", "0:76", "A:3525623658;C:2869684594;G:2708534500;T:2083102664;N:159660", 76, null, null, null, 3525623658, 2869684594, 2708534500, 2083102664, 159660, "SRX4168707", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43087, "SRR7264591", "SRX4168706", "SRS3380685", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated", null, "strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "AG01046.6;AG01047.6;AG01049.6;unrelated", "AG01046.6;AG01047.6;AG01049.6;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HBCAFADXX_JBBS71_021_R1.fastq.gz", "fastq", 5103002976.0, 67144776.0, "HBCAFADXX JBBS71 021 R1.fastq.gz", "0:76", "A:1565087315;C:1292145008;G:1214936605;T:1030712352;N:121696", 76, null, null, null, 1565087315, 1292145008, 1214936605, 1030712352, 121696, "SRX4168706", "SRS3380685", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 2e-05, null, 1e-05, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43088, "SRR7264592", "SRX4168705", "SRS3380685", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated", null, "strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "AG01046.5;AG01047.5;AG01049.5;unrelated", "AG01046.5;AG01047.5;AG01049.5;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "C562AACXX_JBBS71_NOBCX_R1.fastq.gz", "fastq", 11245730944.0, 147970144.0, "C562AACXX JBBS71 NOBCX R1.fastq.gz", "0:76", "A:3451642355;C:2826476753;G:2670179644;T:2277897894;N:19534298", 76, null, null, null, 3451642355, 2826476753, 2670179644, 2277897894, 19534298, "SRX4168705", "SRS3380685", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43089, "SRR7264593", "SRX4168704", "SRS3380684", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "AG01269.2;AG01270.2", "AG01269.2;AG01270.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVK53ADXX_JBCX101_016_R1.fastq.gz", "fastq", 4318423208.0, 56821358.0, "HVK53ADXX JBCX101 016 R1.fastq.gz", "0:76", "A:1370691469;C:1101595011;G:1048719303;T:796936406;N:481019", 76, null, null, null, 1370691469, 1101595011, 1048719303, 796936406, 481019, "SRX4168704", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 1e-05, null, 0.0, null, 0.99997, null, 0.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43090, "SRR7264594", "SRX4168703", "SRS3380684", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "AG01269.1;AG01270.1", "AG01269.1;AG01270.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HMHGVADXX_JBCX101_016_R1.fastq.gz", "fastq", 3247405520.0, 42729020.0, "HMHGVADXX JBCX101 016 R1.fastq.gz", "0:76", "A:1030573532;C:829398246;G:789085434;T:598013908;N:334400", 76, null, null, null, 1030573532, 829398246, 789085434, 598013908, 334400, "SRX4168703", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43091, "SRR7264595", "SRX4168702", "SRS3380683", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "AG01428.5;AG01429.5", "AG01428.5;AG01429.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HJTYNBCXX_JBDG110_NOBCX_R1.fastq.gz", "fastq", 8473348224.0, 111491424.0, "HJTYNBCXX JBDG110 NOBCX R1.fastq.gz", "0:76", "A:2738474380;C:2086110939;G:1986494866;T:1661471870;N:796169", 76, null, null, null, 2738474380, 2086110939, 1986494866, 1661471870, 796169, "SRX4168702", "SRS3380683", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 3e-05, null, 2e-05, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43092, "SRR7264596", "SRX4168701", "SRS3380683", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "AG01428.4;AG01429.4", "AG01428.4;AG01429.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJ7NADXX_JBDG110_013_R1.fastq.gz", "fastq", 1317100672.0, 17330272.0, "HVJ7NADXX JBDG110 013 R1.fastq.gz", "0:76", "A:424319849;C:318879376;G:308835829;T:264971153;N:94465", 76, null, null, null, 424319849, 318879376, 308835829, 264971153, 94465, "SRX4168701", "SRS3380683", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 9e-05, null, 5e-05, null, 0.99995, null, 0.2, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43093, "SRR5893052", "SRX3058793", "SRS2404523", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA   6h a Am pA RNA B1", "miniresa AG01714", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|replicate group:27|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA   6h a Am pA RNA B1", "AG01714.1", "AG01714.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01714.1_R1.fastq.gz", "fastq", 263900576.0, 3472376.0, "AG01714.1 R1.fastq.gz", "0:76", "A:71973779;C:48927629;G:51913512;T:91079622;N:6034", 76, null, null, null, 71973779, 48927629, 51913512, 91079622, 6034, "SRX3058793", "SRS2404523", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.9163, null, 3e-05, null, 0.99833, null, 0.61085, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43094, "SRR5893053", "SRX3058792", "SRS2404525", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA   6h a Am pA RNA B2", "miniresa AG01715", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|replicate group:27|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA   6h a Am pA RNA B2", "AG01715.1", "AG01715.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01715.1_R1.fastq.gz", "fastq", 233910976.0, 3077776.0, "AG01715.1 R1.fastq.gz", "0:76", "A:63827548;C:43163354;G:46127646;T:80731865;N:60563", 76, null, null, null, 63827548, 43163354, 46127646, 80731865, 60563, "SRX3058792", "SRS2404525", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.92571, null, 3e-05, null, 0.99809, null, 0.62106, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43095, "SRR5893054", "SRX3058791", "SRS2404524", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA   2h pA RNA B1", "miniresa AG01710", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:25|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA   2h pA RNA B1", "AG01710.1", "AG01710.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01710.1_R1.fastq.gz", "fastq", 236178588.0, 3107613.0, "AG01710.1 R1.fastq.gz", "0:76", "A:63902747;C:43772893;G:46507615;T:81990822;N:4511", 76, null, null, null, 63902747, 43772893, 46507615, 81990822, 4511, "SRX3058791", "SRS2404524", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.92111, null, 4e-05, null, 0.99799, null, 0.56316, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43096, "SRR5893055", "SRX3058790", "SRS2404526", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA   2h pA RNA B2", "miniresa AG01711", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:25|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA   2h pA RNA B2", "AG01711.1", "AG01711.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01711.1_R1.fastq.gz", "fastq", 226089360.0, 2974860.0, "AG01711.1 R1.fastq.gz", "0:76", "A:61341697;C:41846683;G:44622362;T:78273216;N:5402", 76, null, null, null, 61341697, 41846683, 44622362, 78273216, 5402, "SRX3058790", "SRS2404526", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.91845, null, 1e-05, null, 0.99797, null, 0.60522, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43097, "SRR5893056", "SRX3058789", "SRS2404529", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA   6h pA RNA B1", "miniresa AG01712", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:26|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA   6h pA RNA B1", "AG01712.1", "AG01712.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01712.1_R1.fastq.gz", "fastq", 247808716.0, 3260641.0, "AG01712.1 R1.fastq.gz", "0:76", "A:67604374;C:45731516;G:48975112;T:85491937;N:5777", 76, null, null, null, 67604374, 45731516, 48975112, 85491937, 5777, "SRX3058789", "SRS2404529", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.91668, null, 4e-05, null, 0.99837, null, 0.57941, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43098, "SRR5893057", "SRX3058788", "SRS2404527", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA   6h pA RNA B2", "miniresa AG01713", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:26|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA   6h pA RNA B2", "AG01713.1", "AG01713.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01713.1_R1.fastq.gz", "fastq", 314337748.0, 4136023.0, "AG01713.1 R1.fastq.gz", "0:76", "A:86391705;C:58569607;G:62248447;T:107120293;N:7696", 76, null, null, null, 86391705, 58569607, 62248447, 107120293, 7696, "SRX3058788", "SRS2404527", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.88475, null, 1e-05, null, 0.99845, null, 0.62559, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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"], [43105, "SRR5893072", "SRX3058773", "SRS2404537", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT shield in vivo", "dmsseq AG01044", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT shield in vivo", "AG01044.6", "AG01044.6", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01044.6_R1.fastq.gz", "fastq", 352399237.0, 15002980.0, "AG01044.6 R1.fastq.gz", "0:23.49 1:0", "A:95827007;C:78301278;G:87345623;T:90923434;N:1895", 23, 0, null, null, 95827007, 78301278, 87345623, 90923434, 1895, "SRX3058773", "SRS2404537", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.57991, null, 0.14096, null, 0.78833, null, 0.59313, null, 19, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43106, "SRR5893073", "SRX3058772", "SRS2404537", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT shield in vivo", "dmsseq AG01044", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT shield in vivo", "AG01044.5", "AG01044.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01044.5_R1.fastq.gz", "fastq", 1345288777.0, 56803082.0, "AG01044.5 R1.fastq.gz", "0:23.68 1:0", "A:365900523;C:297605434;G:332516082;T:349160736;N:106002", 23, 0, null, null, 365900523, 297605434, 332516082, 349160736, 106002, "SRX3058772", "SRS2404537", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.58577, null, 0.1419, null, 0.7875, null, 0.55349, null, 34, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43107, "SRR5893074", "SRX3058771", "SRS2404537", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT shield in vivo", "dmsseq AG01044", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT shield in vivo", "AG01044.4", "AG01044.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01044.4_R1.fastq.gz", "fastq", 914428539.0, 38790299.0, "AG01044.4 R1.fastq.gz", "0:23.57 1:0", "A:247816262;C:203789970;G:226994244;T:235814929;N:13134", 23, 0, null, null, 247816262, 203789970, 226994244, 235814929, 13134, "SRX3058771", "SRS2404537", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.58479, null, 0.14134, null, 0.7895, null, 0.58758, null, 17, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43108, "SRR5893075", "SRX3058770", "SRS2404537", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT shield in vivo", "dmsseq AG01044", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT shield in vivo", "AG01044.3", "AG01044.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01044.3_R1.fastq.gz", "fastq", 788379216.0, 33454094.0, "AG01044.3 R1.fastq.gz", "0:23.57 1:0", "A:213097014;C:176081523;G:196161554;T:203036893;N:2232", 23, 0, null, null, 213097014, 176081523, 196161554, 203036893, 2232, "SRX3058770", "SRS2404537", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.58292, null, 0.13842, null, 0.78975, null, 0.59022, null, 16, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43109, "SRR5893076", "SRX3058769", "SRS2404537", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT shield in vivo", "dmsseq AG01044", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT shield in vivo", "AG01044.2", "AG01044.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01044.2_R1.fastq.gz", "fastq", 53616540.0, 2286483.0, "AG01044.2 R1.fastq.gz", "0:23.45 1:0", "A:14492308;C:11955609;G:13424134;T:13741847;N:2642", 23, 0, null, null, 14492308, 11955609, 13424134, 13741847, 2642, "SRX3058769", "SRS2404537", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.56568, null, 0.13601, null, 0.79101, null, 0.59727, null, 26, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43110, "SRR5893077", "SRX3058768", "SRS2404537", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT shield in vivo", "dmsseq AG01044", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT shield in vivo", "AG01044.1", "AG01044.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01044.1_R1.fastq.gz", "fastq", 157041129.0, 6654774.0, "AG01044.1 R1.fastq.gz", "0:23.60 1:0", "A:42428242;C:35110921;G:39122952;T:40378347;N:667", 23, 0, null, null, 42428242, 35110921, 39122952, 40378347, 667, "SRX3058768", "SRS2404537", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.58493, null, 0.13991, null, 0.78735, null, 0.59014, null, 15, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43111, "SRR5893078", "SRX3058767", "SRS2404538", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT sphere in vivo", "dmsseq AG01043", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT sphere in vivo", "AG01043.6", "AG01043.6", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01043.6_R1.fastq.gz", "fastq", 245591088.0, 10387582.0, "AG01043.6 R1.fastq.gz", "0:23.64 1:0", "A:66848740;C:56927652;G:60996703;T:60816631;N:1362", 23, 0, null, null, 66848740, 56927652, 60996703, 60816631, 1362, "SRX3058767", "SRS2404538", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.62265, null, 0.12438, null, 0.7696, null, 0.59474, null, 32, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43112, "SRR5893079", "SRX3058766", "SRS2404538", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT sphere in vivo", "dmsseq AG01043", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT sphere in vivo", "AG01043.5", "AG01043.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01043.5_R1.fastq.gz", "fastq", 935516222.0, 39234795.0, "AG01043.5 R1.fastq.gz", "0:23.84 1:0", "A:254864411;C:216185186;G:231676738;T:232716892;N:72995", 23, 0, null, null, 254864411, 216185186, 231676738, 232716892, 72995, "SRX3058766", "SRS2404538", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.6326, null, 0.12713, null, 0.76739, null, 0.59812, null, 27, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43113, "SRR5893080", "SRX3058765", "SRS2404538", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT sphere in vivo", "dmsseq AG01043", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT sphere in vivo", "AG01043.4", "AG01043.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01043.4_R1.fastq.gz", "fastq", 633932186.0, 26698352.0, "AG01043.4 R1.fastq.gz", "0:23.74 1:0", "A:172078766;C:147459021;G:157655737;T:156729321;N:9341", 23, 0, null, null, 172078766, 147459021, 157655737, 156729321, 9341, "SRX3058765", "SRS2404538", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.62892, null, 0.12689, null, 0.76915, null, 0.59625, null, 19, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43114, "SRR5893081", "SRX3058764", "SRS2404538", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT sphere in vivo", "dmsseq AG01043", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT sphere in vivo", "AG01043.3", "AG01043.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01043.3_R1.fastq.gz", "fastq", 545501906.0, 22980935.0, "AG01043.3 R1.fastq.gz", "0:23.74 1:0", "A:147643154;C:127194084;G:135926112;T:134737007;N:1549", 23, 0, null, null, 147643154, 127194084, 135926112, 134737007, 1549, "SRX3058764", "SRS2404538", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.63069, null, 0.12544, null, 0.76781, null, 0.60018, null, 26, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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"], [43125, "SRR5893092", "SRX3058753", "SRS2404538", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT sphere in vivo", "dmsseq AG01043", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT sphere in vivo", "AG01043.1", "AG01043.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01043.1_R1.fastq.gz", "fastq", 108747256.0, 4575669.0, "AG01043.1 R1.fastq.gz", "0:23.77 1:0", "A:29414532;C:25366431;G:27139739;T:26826074;N:480", 23, 0, null, null, 29414532, 25366431, 27139739, 26826074, 480, "SRX3058753", "SRS2404538", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.62913, null, 0.12566, null, 0.76946, null, 0.59653, null, 20, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43126, "SRR5893093", "SRX3058752", "SRS2404538", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT sphere in vivo", "dmsseq AG01043", null, "strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:15|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT sphere in vivo", "AG01043.2", "AG01043.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01043.2_R1.fastq.gz", "fastq", 37331204.0, 1581621.0, "AG01043.2 R1.fastq.gz", "0:23.60 1:0", "A:10098397;C:8686566;G:9362492;T:9181793;N:1956", 23, 0, null, null, 10098397, 8686566, 9362492, 9181793, 1956, "SRX3058752", "SRS2404538", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.60497, null, 0.12042, null, 0.77114, null, 0.5559, null, 21, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43127, "SRR5893094", "SRX3058751", "SRS2404542", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT 64c in vivo", "dmsseq AG01042", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT 64c in vivo", "AG01042.1", "AG01042.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01042.1_R1.fastq.gz", "fastq", 126429566.0, 5343149.0, "AG01042.1 R1.fastq.gz", "0:23.66 1:0", "A:33794193;C:29213503;G:32293032;T:31128226;N:612", 23, 0, null, null, 33794193, 29213503, 32293032, 31128226, 612, "SRX3058751", "SRS2404542", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.60436, null, 0.07589, null, 0.78179, null, 0.58081, null, 23, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43128, "SRR5893095", "SRX3058750", "SRS2404542", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT 64c in vivo", "dmsseq AG01042", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT 64c in vivo", "AG01042.2", "AG01042.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01042.2_R1.fastq.gz", "fastq", 43162881.0, 1835075.0, "AG01042.2 R1.fastq.gz", "0:23.52 1:0", "A:11533531;C:9954515;G:11073245;T:10599502;N:2088", 23, 0, null, null, 11533531, 9954515, 11073245, 10599502, 2088, "SRX3058750", "SRS2404542", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.58191, null, 0.07361, null, 0.78255, null, 0.5884, null, 27, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43129, "SRR5893096", "SRX3058749", "SRS2404532", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT 64c DMScontrol in vitro", "dmsseq AG00876", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:water in vitro|molecule:RNA|selection:pA|condition:control|replicate group:13|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT 64c DMScontrol in vitro", "AG00876.3", "AG00876.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG00876.3_R1.fastq.gz", "fastq", 981554972.0, 12915197.0, "AG00876.3 R1.fastq.gz", "0:76", "A:261237433;C:277515571;G:240090014;T:202665429;N:46525", 76, null, null, null, 261237433, 277515571, 240090014, 202665429, 46525, "SRX3058749", "SRS2404532", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 2e-05, null, 0.0, null, 0.99995, null, 1.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43130, "SRR5893097", "SRX3058748", "SRS2404532", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT 64c DMScontrol in vitro", "dmsseq AG00876", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:water in vitro|molecule:RNA|selection:pA|condition:control|replicate group:13|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT 64c DMScontrol in vitro", "AG00876.4", "AG00876.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG00876.4_R1.fastq.gz", "fastq", 662935688.0, 8722838.0, "AG00876.4 R1.fastq.gz", "0:76", "A:176751346;C:187148186;G:162147575;T:136873146;N:15435", 76, null, null, null, 176751346, 187148186, 162147575, 136873146, 15435, "SRX3058748", "SRS2404532", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43131, "SRR5893098", "SRX3058747", "SRS2404542", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT 64c in vivo", "dmsseq AG01042", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT 64c in vivo", "AG01042.5", "AG01042.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01042.5_R1.fastq.gz", "fastq", 1080031154.0, 45488589.0, "AG01042.5 R1.fastq.gz", "0:23.74 1:0", "A:290744683;C:247189003;G:273714462;T:268297982;N:85024", 23, 0, null, null, 290744683, 247189003, 273714462, 268297982, 85024, "SRX3058747", "SRS2404542", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.60791, null, 0.07492, null, 0.77979, null, 0.58326, null, 29, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43132, "SRR5893099", "SRX3058746", "SRS2404542", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT 64c in vivo", "dmsseq AG01042", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT 64c in vivo", "AG01042.6", "AG01042.6", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01042.6_R1.fastq.gz", "fastq", 283394970.0, 12033965.0, "AG01042.6 R1.fastq.gz", "0:23.55 1:0", "A:76195456;C:65114236;G:72044677;T:70039067;N:1534", 23, 0, null, null, 76195456, 65114236, 72044677, 70039067, 1534, "SRX3058746", "SRS2404542", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.59876, null, 0.07667, null, 0.78135, null, 0.58397, null, 33, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43133, "SRR5893100", "SRX3058745", "SRS2404542", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT 64c in vivo", "dmsseq AG01042", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT 64c in vivo", "AG01042.3", "AG01042.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01042.3_R1.fastq.gz", "fastq", 635217690.0, 26879456.0, "AG01042.3 R1.fastq.gz", "0:23.63 1:0", "A:169915710;C:146718321;G:161940079;T:156641690;N:1890", 23, 0, null, null, 169915710, 146718321, 161940079, 156641690, 1890, "SRX3058745", "SRS2404542", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.60186, null, 0.07604, null, 0.78186, null, 0.58928, null, 29, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43134, "SRR5893101", "SRX3058744", "SRS2404542", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT 64c in vivo", "dmsseq AG01042", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT 64c in vivo", "AG01042.4", "AG01042.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01042.4_R1.fastq.gz", "fastq", 737360617.0, 31187809.0, "AG01042.4 R1.fastq.gz", "0:23.64 1:0", "A:197816552;C:169921394;G:187620043;T:181992000;N:10628", 23, 0, null, null, 197816552, 169921394, 187620043, 181992000, 10628, "SRX3058744", "SRS2404542", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.60088, null, 0.07706, null, 0.78046, null, 0.547, null, 15, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43135, "SRR5893102", "SRX3058743", "SRS2404543", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT shield in vivo", "dmsseq AG01047", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT shield in vivo", "AG01047.3", "AG01047.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01047.3_R1.fastq.gz", "fastq", 688382781.0, 30034225.0, "AG01047.3 R1.fastq.gz", "0:22.92 1:0", "A:189019980;C:152064230;G:163028336;T:184268177;N:2058", 22, 0, null, null, 189019980, 152064230, 163028336, 184268177, 2058, "SRX3058743", "SRS2404543", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.57527, null, 0.14405, null, 0.7892, null, 0.59515, null, 16, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43136, "SRR5893103", "SRX3058742", "SRS2404543", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT shield in vivo", "dmsseq AG01047", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT shield in vivo", "AG01047.4", "AG01047.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01047.4_R1.fastq.gz", "fastq", 786863431.0, 34313776.0, "AG01047.4 R1.fastq.gz", "0:22.93 1:0", "A:216579236;C:173455382;G:185880723;T:210944466;N:3624", 22, 0, null, null, 216579236, 173455382, 185880723, 210944466, 3624, "SRX3058742", "SRS2404543", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.57576, null, 0.14501, null, 0.79026, null, 0.5962, null, 25, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43137, "SRR5893104", "SRX3058741", "SRS2404544", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT 64c in vivo", "dmsseq AG01046", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT 64c in vivo", "AG01046.1", "AG01046.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01046.1_R1.fastq.gz", "fastq", 104571264.0, 4565699.0, "AG01046.1 R1.fastq.gz", "0:22.90 1:0", "A:26920338;C:24177052;G:26506298;T:26967196;N:380", 22, 0, null, null, 26920338, 24177052, 26506298, 26967196, 380, "SRX3058741", "SRS2404544", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.5641, null, 0.06574, null, 0.78437, null, 0.58268, null, 15, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43138, "SRR5893105", "SRX3058740", "SRS2404544", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS Seq   WT 64c in vivo", "dmsseq AG01046", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   WT 64c in vivo", "AG01046.2", "AG01046.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "AG01046.2_R1.fastq.gz", "fastq", 34508189.0, 1516870.0, "AG01046.2 R1.fastq.gz", "0:22.75 1:0", "A:8891670;C:7954125;G:8796911;T:8864593;N:890", 22, 0, null, null, 8891670, 7954125, 8796911, 8864593, 890, "SRX3058740", "SRS2404544", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.54153, null, 0.06305, null, 0.7852, null, 0.5792, null, 19, 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