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736 rows where experiment.library_selection = "unspecified" and tissue_curation = "Embryo Imprecise"

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devstage_curation 10

experiment.library_strategy 3

technology 2

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devstage_curation_coarse 2

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tissue_curation 1

  • Embryo Imprecise · 736 ✖

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  • unspecified · 736 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
8055 8055 ERR022484 ERX008924 ERS017427 ERP000400 PRJEB2333 Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E-MTAB-434 Other         E MTAB 434:ZF 2cells SAMEA898400 Wellcome Sanger Institute Alias:E MTAB 434:ZF 2cells|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 03 10T17:55:05Z|INSDC last update:2018 03 08T15:25:14Z|INSDC status:public|SRA accession:ERS017427|Sample Name:ERS017427|Sex:mixed|StrainOrLine:Tuebingen|Title:ZF 2cells                 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E MTAB 434:sequencing of Zebrafish embryo 2cells RNA from Zebrafish embryo 2cells Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp. Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:cell FL-cDNA TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000400 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16 4946_5.srf srf 3947547008.0 25970704.0 E MTAB 434:4946 5.srf 0:76 1:76 A:1069302461;C:914233601;G:902631356;T:1055986090;N:5393500 76 76     1069302461 914233601 902631356 1055986090 5393500 ERX008924 ERS017427 ERA015179 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.93356 0.93346 0.03988 0.04022 0.79135 0.79198 0.48864 0.48464 76 76 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2011-03-10 Cleavage Embryo Embryo Imprecise All anatomical structures
36405 36405 SRR546820 SRX180750 SRS347212 SRP013950 PRJNA169500 Danio rerio embryonic promoterome PRJNA169500 Transcriptome Analysis Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.   pubmed:24531765 Zebrafish wild type AB strain embryo prim6 stage D. rerio prim6 embryo D. rerio prim6 embryo                     RNAseq D. rerio prim6 embryo RNAseq D. rerio prim6 embryo 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013950     RNAseq_prim6_2_fix.fastq fastq 3011340704.0 19811452.0 RNAseq D. rerio prim6 embryo 0:76 1:76 A:727345664;C:767747833;G:787766862;T:725606403;N:2873942 76 76     727345664 767747833 787766862 725606403 2873942 SRX180750 SRS347212 SRA055273 University of Bergen ZEPROME consortium 2 0.94491 0.94492 0.04196 0.04323 0.76641 0.76928 0.48087 0.48787 76 76 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   Unknown 2015-07-22 Undetermined Embryo Embryo Imprecise All anatomical structures
36406 36406 SRR546819 SRX180749 SRS347211 SRP013950 PRJNA169500 Danio rerio embryonic promoterome PRJNA169500 Transcriptome Analysis Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.   pubmed:24531765 Zebrafish wild type AB strain embryo 14 somites stage D. rerio 14 somites embryo D. rerio 14 somites embryo                     RNAseq D. rerio 14 somites embryo RNAseq D. rerio 14 somites embryo 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013950     RNAseq_14somites_2.fastq fastq 2976465520.0 19582010.0 RNAseq D. rerio 14 somites embryo 0:76 1:76 A:747831748;C:733533938;G:754151936;T:738091995;N:2855903 76 76     747831748 733533938 754151936 738091995 2855903 SRX180749 SRS347211 SRA055273 University of Bergen ZEPROME consortium 2 0.9236 0.91427 0.0861 0.08534 0.7559 0.75528 0.48428 0.47549 76 76 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   Unknown 2015-07-22 Segmentation Embryo Embryo Imprecise All anatomical structures
36407 36407 SRR546818 SRX180748 SRS347209 SRP013950 PRJNA169500 Danio rerio embryonic promoterome PRJNA169500 Transcriptome Analysis Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.   pubmed:24531765 Zebrafish wild type AB strain embryo dome/zfs:0000015 stage D. rerio dome/zfs:0000015 embryo D. rerio dome/zfs:0000015 embryo                     RNAseq D. rerio dome/zfs:0000015 embryo RNAseq D. rerio dome/zfs:0000015 embryo 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013950     RNAseq_30p_dome_1.fastq fastq 2359648608.0 15524004.0 RNAseq D. rerio dome/zfs:0000015 embryo 0:76 1:76 A:588562906;C:575605218;G:603310130;T:589755481;N:2414873 76 76     588562906 575605218 603310130 589755481 2414873 SRX180748 SRS347209 SRA055273 University of Bergen ZEPROME consortium 2 0.89779 0.9222 0.04122 0.0431 0.76609 0.77112 0.49779 0.49305 76 76 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   Unknown 2015-07-22 Blastula Embryo Embryo Imprecise All anatomical structures
36408 36408 SRR546817 SRX180747 SRS358988 SRP013950 PRJNA169500 Danio rerio embryonic promoterome PRJNA169500 Transcriptome Analysis Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.   pubmed:24531765 Zebrafish wild type AB strain embryo 2 cells stage D. rerio 2 cells embryo D. rerio 2 cells embryo                     RNAseq D. rerio 2 cells embryo RNAseq D. rerio 2 cells embryo 1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013950         2799828144.0 18419922.0 RNAseq D. rerio 2 cells embryo 0:76 1:76 A:678251421;C:711410510;G:729905459;T:677312772;N:2947982 76 76     678251421 711410510 729905459 677312772 2947982 SRX180747 SRS358988 SRA055273 University of Bergen ZEPROME consortium 2 0.9498 0.94704 0.02363 0.02442 0.7988 0.80221 0.48657 0.49361 76 76 B B biological fallback assumption illumina early_illumina unknown unknown unknown bulk unknown unknown   Unknown 2015-07-22 Cleavage Embryo Embryo Imprecise All anatomical structures
36581 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.     1 Test GFP Negative 1                     Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development Embryos 1 1     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         2525199228.0 65962848.0 GFP Positive 0:38.28 A:665802914;C:594493287;G:612298433;T:652078696;N:525898 38       665802914 594493287 612298433 652078696 525898 SRX195432 SRS369361     University of Cambridge 1 0.89062   0.09595   0.74059   0.47506   36   B   usable mapping rate illumina early_illumina unknown unknown unknown bulk unknown unknown   United Kingdom 2015-07-22 Undetermined Embryo Embryo Imprecise All anatomical structures
36582 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.     1 Test GFP Negative 1                     Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development Embryos 1 1     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     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       686329592 587342682 601330559 674194074 485241 SRX195432 SRS369361     University of Cambridge 1 0.90413   0.13272   0.71342   0.48186   36   B   usable mapping rate illumina early_illumina unknown unknown unknown bulk unknown unknown   United Kingdom 2015-07-22 Undetermined Embryo Embryo Imprecise All anatomical structures
41381 41381 SRR4375307 SRX2226800 SRS1732678 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 64c B1 resa AG01072   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal                 RESA Seq Mut 64c B1 AG01072.1 AG01072.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01072.1_R1.fastq.gz AG01072.1_R2.fastq.gz fastq fastq 756436968.0 4976559.0 AG01072.1 R2.fastq.gz 0:76 1:76 A:277813562;C:101592220;G:103435859;T:273576694;N:18633 76 76     277813562 101592220 103435859 273576694 18633 SRX2226800 SRS1732678 SRA482696 Yale University|Genetics Yale University 2 0.00777 0.00795 0.00043 0.00056 0.99344 0.99389 0.43869 0.43095 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-10-06 Undetermined Embryo Embryo Imprecise All anatomical structures
41382 41382 SRR4375306 SRX2226799 SRS1732692 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq WT 8h pA r3 B3 resa AG01070   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal                 RESA Seq WT 8h pA r3 B3 AG01070.1 AG01070.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01070.1_R1.fastq.gz AG01070.1_R2.fastq.gz fastq fastq 601712368.0 3958634.0 AG01070.1 R2.fastq.gz 0:76 1:76 A:188474921;C:113643606;G:114382568;T:185195364;N:15909 76 76     188474921 113643606 114382568 185195364 15909 SRX2226799 SRS1732692 SRA482696 Yale University|Genetics Yale University 2 0.84037 0.84016 0.03493 0.03544 0.97303 0.97252 0.46337 0.47093 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41383 41383 SRR4375305 SRX2226798 SRS1732691 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq WT 8h pA r3 B2 resa AG01069   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal                 RESA Seq WT 8h pA r3 B2 AG01069.1 AG01069.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01069.1_R1.fastq.gz AG01069.1_R2.fastq.gz fastq fastq 1344477848.0 8845249.0 AG01069.1 R1.fastq.gz 0:76 1:76 A:418545593;C:256422789;G:257715519;T:411760293;N:33654 76 76     418545593 256422789 257715519 411760293 33654 SRX2226798 SRS1732691 SRA482696 Yale University|Genetics Yale University 2 0.84542 0.84566 0.03642 0.03588 0.97084 0.97197 0.4739 0.48121 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41384 41384 SRR4375304 SRX2226797 SRS1732690 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq WT 8h pA r3 B1 resa AG01068   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal                 RESA Seq WT 8h pA r3 B1 AG01068.1 AG01068.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01068.1_R1.fastq.gz AG01068.1_R2.fastq.gz fastq fastq 896200056.0 5896053.0 AG01068.1 R2.fastq.gz 0:76 1:76 A:278768309;C:171161843;G:172303088;T:273944252;N:22564 76 76     278768309 171161843 172303088 273944252 22564 SRX2226797 SRS1732690 SRA482696 Yale University|Genetics Yale University 2 0.83862 0.83897 0.0351 0.03585 0.97183 0.97204 0.47364 0.47138 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41385 41385 SRR4375303 SRX2226796 SRS1732689 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq WT 8h L430 pA r3 B3 resa AG01067   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr tinyLNA miR 430|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal                 RESA Seq WT 8h L430 pA r3 B3 AG01067.1 AG01067.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01067.1_R1.fastq.gz AG01067.1_R2.fastq.gz fastq fastq 1799778192.0 11840646.0 AG01067.1 R1.fastq.gz 0:76 1:76 A:561491448;C:342221462;G:343998479;T:552022535;N:44268 76 76     561491448 342221462 343998479 552022535 44268 SRX2226796 SRS1732689 SRA482696 Yale University|Genetics Yale University 2 0.84432 0.84397 0.03554 0.03522 0.97224 0.9725 0.46732 0.46922 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41386 41386 SRR4375302 SRX2226795 SRS1732688 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq WT 8h L430 pA r3 B2 resa AG01066   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr tinyLNA miR 430|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal                 RESA Seq WT 8h L430 pA r3 B2 AG01066.1 AG01066.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01066.1_R1.fastq.gz AG01066.1_R2.fastq.gz fastq fastq 1313436864.0 8641032.0 AG01066.1 R2.fastq.gz 0:76 1:76 A:409666264;C:249755645;G:251028600;T:402953610;N:32745 76 76     409666264 249755645 251028600 402953610 32745 SRX2226795 SRS1732688 SRA482696 Yale University|Genetics Yale University 2 0.84584 0.84611 0.0349 0.03543 0.97189 0.97175 0.47547 0.48555 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41387 41387 SRR4375301 SRX2226794 SRS1732687 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq WT 8h L430 pA r3 B1 resa AG01065   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr tinyLNA miR 430|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal                 RESA Seq WT 8h L430 pA r3 B1 AG01065.1 AG01065.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01065.1_R2.fastq.gz AG01065.1_R1.fastq.gz fastq fastq 1442385152.0 9489376.0 AG01065.1 R2.fastq.gz 0:76 1:76 A:449362282;C:274879749;G:276626223;T:441480173;N:36725 76 76     449362282 274879749 276626223 441480173 36725 SRX2226794 SRS1732687 SRA482696 Yale University|Genetics Yale University 2 0.8417 0.84205 0.03519 0.03559 0.97193 0.97179 0.47697 0.46118 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41388 41388 SRR4375300 SRX2226793 SRS1732685 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA CLIP Ago2 RESA CLIP Ago2 input resa clip ago2 AG01631   strain:TU/AB|age:4.7|dev stage:zfs:0000015|sex:pooled male and female|tissue:embryo|treatment:500UTR flag ago2 crosslink|molecule:RNA|selection:5% input before pulldown|condition:input|BioSampleModel:Model organism or animal                 RESA CLIP Ago2 RESA CLIP Ago2 input AG01631.1 AG01631.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01631.1_R1.fastq.gz AG01631.1_R2.fastq.gz fastq fastq 9864834960.0 64900230.0 AG01631.1 R2.fastq.gz 0:76 1:76 A:2990534603;C:1958949912;G:1963153108;T:2951932817;N:264520 76 76     2990534603 1958949912 1963153108 2951932817 264520 SRX2226793 SRS1732685 SRA482696 Yale University|Genetics Yale University 2 0.83121 0.85078 0.03505 0.0364 0.97171 0.97019 0.46925 0.47246 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Blastula Embryo Embryo Imprecise All anatomical structures
41389 41389 SRR4375299 SRX2226779 SRS1732684 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA CLIP Ago2 RESA CLIP Ago2 IP resa clip ago2 AG01630   strain:TU/AB|age:4.7|dev stage:zfs:0000015|sex:pooled male and female|tissue:embryo|treatment:500UTR flag ago2 crosslink|molecule:RNA|selection:flag bead pulldown post crosslinking|condition:Ago2 IP|BioSampleModel:Model organism or animal                 RESA CLIP Ago2 RESA CLIP Ago2 IP AG01630.1 AG01630.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01630.1_R1.fastq.gz AG01630.1_R2.fastq.gz fastq fastq 9348207632.0 61501366.0 AG01630.1 R1.fastq.gz 0:76 1:76 A:2819572908;C:1871537719;G:1881735941;T:2775115216;N:245848 76 76     2819572908 1871537719 1881735941 2775115216 245848 SRX2226779 SRS1732684 SRA482696 Yale University|Genetics Yale University 2 0.80207 0.78648 0.02992 0.02839 0.97885 0.97871 0.49297 0.49107 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Blastula Embryo Embryo Imprecise All anatomical structures
41390 41390 SRR4375197 SRX2226727 SRS1732683 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 8h B3 resa AG01086   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal                 RESA Seq Mut 8h B3 AG01086.2 AG01086.2 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01086.2_R1.fastq.gz AG01086.2_R2.fastq.gz fastq fastq 714848400.0 4702950.0 AG01086.2 R2.fastq.gz 0:76 1:76 A:261928616;C:96586565;G:97768464;T:258351392;N:213363 76 76     261928616 96586565 97768464 258351392 213363 SRX2226727 SRS1732683 SRA482696 Yale University|Genetics Yale University 2 0.00715 0.00733 0.00046 0.00044 0.99417 0.99435 0.46775 0.42207 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41391 41391 SRR4375176 SRX2226710 SRS1732686 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq WT 64c pA r3 B2 resa AG01061   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal                 RESA Seq WT 64c pA r3 B2 AG01061.1 AG01061.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01061.1_R1.fastq.gz AG01061.1_R2.fastq.gz fastq fastq 724448416.0 4766108.0 AG01061.1 R2.fastq.gz 0:76 1:76 A:224701149;C:138989041;G:139762199;T:220977796;N:18231 76 76     224701149 138989041 139762199 220977796 18231 SRX2226710 SRS1732686 SRA482696 Yale University|Genetics Yale University 2 0.84913 0.84756 0.03557 0.03568 0.97153 0.97116 0.47281 0.46157 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-10-06 Cleavage Embryo Embryo Imprecise All anatomical structures
41392 41392 SRR4375175 SRX2226709 SRS1732683 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 8h B3 resa AG01086   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal                 RESA Seq Mut 8h B3 AG01086.1 AG01086.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01086.1_R1.fastq.gz AG01086.1_R2.fastq.gz fastq fastq 411922128.0 2710014.0 AG01086.1 R1.fastq.gz 0:76 1:76 A:150812258;C:55795177;G:56809368;T:148495332;N:9993 76 76     150812258 55795177 56809368 148495332 9993 SRX2226709 SRS1732683 SRA482696 Yale University|Genetics Yale University 2 0.00798 0.00746 0.00062 0.00055 0.99385 0.99399 0.44328 0.47308 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41393 41393 SRR4375146 SRX2226694 SRS1732682 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 8h B2 resa AG01085   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal                 RESA Seq Mut 8h B2 AG01085.2 AG01085.2 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01085.2_R1.fastq.gz AG01085.2_R2.fastq.gz fastq fastq 700337720.0 4607485.0 AG01085.2 R1.fastq.gz 0:76 1:76 A:256568404;C:94627005;G:95783677;T:253149693;N:208941 76 76     256568404 94627005 95783677 253149693 208941 SRX2226694 SRS1732682 SRA482696 Yale University|Genetics Yale University 2 0.00733 0.00726 0.00055 0.00048 0.99413 0.99393 0.46893 0.45795 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41394 41394 SRR4375102 SRX2226674 SRS1732682 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 8h B2 resa AG01085   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal                 RESA Seq Mut 8h B2 AG01085.1 AG01085.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01085.1_R1.fastq.gz AG01085.1_R2.fastq.gz fastq fastq 409587712.0 2694656.0 AG01085.1 R1.fastq.gz 0:76 1:76 A:149931448;C:55481183;G:56493706;T:147671446;N:9929 76 76     149931448 55481183 56493706 147671446 9929 SRX2226674 SRS1732682 SRA482696 Yale University|Genetics Yale University 2 0.0079 0.0078 0.00056 0.0005 0.99366 0.99385 0.42647 0.47214 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41395 41395 SRR4375101 SRX2226673 SRS1732681 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 8h B1 resa AG01084   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal                 RESA Seq Mut 8h B1 AG01084.2 AG01084.2 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01084.2_R1.fastq.gz AG01084.2_R2.fastq.gz fastq fastq 396825488.0 2610694.0 AG01084.2 R1.fastq.gz 0:76 1:76 A:145317384;C:53679748;G:54375412;T:143331621;N:121323 76 76     145317384 53679748 54375412 143331621 121323 SRX2226673 SRS1732681 SRA482696 Yale University|Genetics Yale University 2 0.0071 0.00673 0.00044 0.00042 0.99417 0.99419 0.44659 0.45357 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41396 41396 SRR4375100 SRX2226672 SRS1732681 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 8h B1 resa AG01084   strain:TU/AB|age:8.0|dev stage:75% epiboly|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal                 RESA Seq Mut 8h B1 AG01084.1 AG01084.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01084.1_R1.fastq.gz AG01084.1_R2.fastq.gz fastq fastq 236514888.0 1556019.0 AG01084.1 R1.fastq.gz 0:76 1:76 A:86560104;C:32062698;G:32664624;T:85221432;N:6030 76 76     86560104 32062698 32664624 85221432 6030 SRX2226672 SRS1732681 SRA482696 Yale University|Genetics Yale University 2 0.00756 0.00706 0.00061 0.00064 0.99405 0.99419 0.47228 0.48736 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Gastrula Embryo Embryo Imprecise All anatomical structures
41397 41397 SRR4375099 SRX2226671 SRS1732680 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 64c B3 resa AG01074   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal                 RESA Seq Mut 64c B3 AG01074.2 AG01074.2 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01074.2_R1.fastq.gz AG01074.2_R2.fastq.gz fastq fastq 1411678568.0 9287359.0 AG01074.2 R1.fastq.gz 0:76 1:76 A:518452828;C:189515599;G:191777773;T:511511925;N:420443 76 76     518452828 189515599 191777773 511511925 420443 SRX2226671 SRS1732680 SRA482696 Yale University|Genetics Yale University 2 0.00745 0.00729 0.00047 0.00045 0.99405 0.99411 0.43814 0.47981 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Undetermined Embryo Embryo Imprecise All anatomical structures
41398 41398 SRR4375098 SRX2226670 SRS1732680 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 64c B3 resa AG01074   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal                 RESA Seq Mut 64c B3 AG01074.1 AG01074.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01074.1_R1.fastq.gz AG01074.1_R2.fastq.gz fastq fastq 867077312.0 5704456.0 AG01074.1 R1.fastq.gz 0:76 1:76 A:318238609;C:116633576;G:118737324;T:313446459;N:21344 76 76     318238609 116633576 118737324 313446459 21344 SRX2226670 SRS1732680 SRA482696 Yale University|Genetics Yale University 2 0.00791 0.00753 0.00052 0.00054 0.99395 0.99381 0.45038 0.44477 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Undetermined Embryo Embryo Imprecise All anatomical structures
41399 41399 SRR4375097 SRX2226669 SRS1732679 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 64c B2 resa AG01073   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal                 RESA Seq Mut 64c B2 AG01073.2 AG01073.2 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01073.2_R1.fastq.gz AG01073.2_R2.fastq.gz fastq fastq 1170921968.0 7703434.0 AG01073.2 R1.fastq.gz 0:76 1:76 A:430252673;C:156958676;G:158824982;T:424542052;N:343585 76 76     430252673 156958676 158824982 424542052 343585 SRX2226669 SRS1732679 SRA482696 Yale University|Genetics Yale University 2 0.00759 0.00753 0.00044 0.00046 0.99389 0.99375 0.48023 0.49305 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Undetermined Embryo Embryo Imprecise All anatomical structures
41400 41400 SRR4375096 SRX2226668 SRS1732679 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 64c B2 resa AG01073   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal                 RESA Seq Mut 64c B2 AG01073.1 AG01073.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01073.1_R1.fastq.gz AG01073.1_R2.fastq.gz fastq fastq 650729936.0 4281118.0 AG01073.1 R1.fastq.gz 0:76 1:76 A:238957997;C:87418913;G:88996057;T:235340339;N:16630 76 76     238957997 87418913 88996057 235340339 16630 SRX2226668 SRS1732679 SRA482696 Yale University|Genetics Yale University 2 0.00771 0.00754 0.00052 0.00049 0.99403 0.9936 0.46484 0.42136 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Undetermined Embryo Embryo Imprecise All anatomical structures
41401 41401 SRR4375095 SRX2226667 SRS1732678 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Mut 64c B1 resa AG01072   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal                 RESA Seq Mut 64c B1 AG01072.2 AG01072.2 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01072.2_R1.fastq.gz AG01072.2_R2.fastq.gz fastq fastq 1293717904.0 8511302.0 AG01072.2 R1.fastq.gz 0:76 1:76 A:475476006;C:173352933;G:175448573;T:469059516;N:380876 76 76     475476006 173352933 175448573 469059516 380876 SRX2226667 SRS1732678 SRA482696 Yale University|Genetics Yale University 2 0.0072 0.0071 0.00042 0.00038 0.99397 0.99385 0.4403 0.43351 76 76 T T mates < 9% mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Undetermined Embryo Embryo Imprecise All anatomical structures
41402 41402 SRR4375094 SRX2226666 SRS1732677 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq WT 64c pA r3 B1 resa AG01060   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal                 RESA Seq WT 64c pA r3 B1 AG01060.1 AG01060.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG01060.1_R1.fastq.gz AG01060.1_R2.fastq.gz fastq fastq 531097120.0 3494060.0 AG01060.1 R1.fastq.gz 0:76 1:76 A:164891814;C:101739900;G:102440303;T:162011179;N:13924 76 76     164891814 101739900 102440303 162011179 13924 SRX2226666 SRS1732677 SRA482696 Yale University|Genetics Yale University 2 0.84523 0.84587 0.03561 0.03503 0.9723 0.97161 0.46204 0.47901 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Cleavage Embryo Embryo Imprecise All anatomical structures
41403 41403 SRR4375093 SRX2226665 SRS1732676 SRP090954 PRJNA345638 RESA identifies mRNA regulatory sequences with high resolution PRJNA345638 Other Gene expression is regulated extensively at the level of mRNA stability localization and translation. However decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here we developed RNA Element Selection Assay RESA a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.       RESA Seq Needle r2 resa AG00580   strain:TU/AB|age:not applicable|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|condition:needle|BioSampleModel:Model organism or animal                 RESA Seq Needle r2 AG00580.1 AG00580.1 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP090954     AG00580.1_R1.fastq.gz AG00580.1_R2.fastq.gz fastq fastq 536691936.0 3530868.0 AG00580.1 R1.fastq.gz 0:76 1:76 A:162711942;C:106417027;G:106484569;T:160130705;N:947693 76 76     162711942 106417027 106484569 160130705 947693 SRX2226665 SRS1732676 SRA482696 Yale University|Genetics Yale University 2 0.85835 0.85877 0.03686 0.03615 0.96818 0.96895 0.47111 0.47948 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-12-31 Undetermined Embryo Embryo Imprecise All anatomical structures
42492 42492 SRR5681431 SRX2916758 SRS2282896 SRP109143 PRJNA389374 Functional role of Eriocalyxin B in zebrafish revealed by transcriptome analysis PRJNA389374 Whole Genome Sequencing the first study to comprehensively explore the effects of EriB in zebrafish model using a transcriptome analysis approach.         15um   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|sex:not determined|tissue:embryos|treatment:15um|BioSampleModel:Model organism or animal                 15um zebrafish 15um zebrafish 15um zebrafish 15um zebrafish     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP109143     15um_2.fq.gz 15um_1.fq.gz fastq fastq 4510379400.0 22551897.0 15um 2.fq.gz 0:100 1:100 A:1183709237;C:1078933188;G:1057042534;T:1190615427;N:79014 100 100     1183709237 1078933188 1057042534 1190615427 79014 SRX2916758 SRS2282896 SRA574072 The Chinese University of HongKong|School of Biomedical Sciences The Chinese University of HongKong 2 0.95073 0.95055 0.0647 0.06526 0.67176 0.67351 0.46247 0.46176 100 100 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   China 2017-06-14 Undetermined Embryo Embryo Imprecise All anatomical structures
42493 42493 SRR5681432 SRX2916757 SRS2282895 SRP109143 PRJNA389374 Functional role of Eriocalyxin B in zebrafish revealed by transcriptome analysis PRJNA389374 Whole Genome Sequencing the first study to comprehensively explore the effects of EriB in zebrafish model using a transcriptome analysis approach.         10um   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|sex:not determined|tissue:embryos|treatment:10um|BioSampleModel:Model organism or animal                 10um zebrafish 10um zebrafish 10um zebrafish 10um zebrafish     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP109143     10um_1.fq.gz 10um_2.fq.gz fastq fastq 4513300800.0 22566504.0 10um 1.fq.gz 0:100 1:100 A:1186008993;C:1078123999;G:1056044415;T:1193043558;N:79835 100 100     1186008993 1078123999 1056044415 1193043558 79835 SRX2916757 SRS2282895 SRA574072 The Chinese University of HongKong|School of Biomedical Sciences The Chinese University of HongKong 2 0.94799 0.94687 0.07002 0.06979 0.66667 0.66746 0.47255 0.47338 100 100 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   China 2017-06-14 Undetermined Embryo Embryo Imprecise All anatomical structures
42494 42494 SRR5681433 SRX2916756 SRS2282894 SRP109143 PRJNA389374 Functional role of Eriocalyxin B in zebrafish revealed by transcriptome analysis PRJNA389374 Whole Genome Sequencing the first study to comprehensively explore the effects of EriB in zebrafish model using a transcriptome analysis approach.         control   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|sex:not determined|tissue:embryos|treatment:control|BioSampleModel:Model organism or animal                 control zebrafish control zebrafish control zebrafish control zebrafish     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 2000   SRP109143     con_1.fq.gz con_2.fq.gz fastq fastq 4514603400.0 22573017.0 con 2.fq.gz 0:100 1:100 A:1183878943;C:1081336890;G:1058805201;T:1190503424;N:78942 100 100     1183878943 1081336890 1058805201 1190503424 78942 SRX2916756 SRS2282894 SRA574072 The Chinese University of HongKong|School of Biomedical Sciences The Chinese University of HongKong 2 0.951 0.95009 0.0669 0.06735 0.6659 0.66681 0.46599 0.46703 100 100 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   China 2017-06-14 Undetermined Embryo Embryo Imprecise All anatomical structures
43058 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.       DMS seq RNA structure positive controls in vitro replicate 1 DMS seq RNA positives ctrl in vitro B1 AG01489   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                 DMS seq RNA structure positive controls in vitro replicate 1 AG01489.1 AG01489.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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     18206335 19464567 21319876 16712584 168 SRX5165478 SRS4174524 SRA825010 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.02389   0.00591   0.97654   0.4758   25   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-12-19 Blastula Embryo Embryo Imprecise All anatomical structures
43059 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.       DMS seq RNA structure positive controls in vitro replicate 2 DMS seq RNA positives ctrl in vitro B2 AG01490   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                 DMS seq RNA structure positive controls in vitro replicate 2 AG01490.1 AG01490.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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     71900468 76519029 81589099 65042019 584 SRX5165477 SRS4174523 SRA825010 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.02362   0.00528   0.98173   0.35096   19   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-12-19 Blastula Embryo Embryo Imprecise All anatomical structures
43060 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       313482382 276309346 291633361 233659719 65320 SRX5165476 SRS4174522 SRA825010 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.00546   0.00047   0.98602   0.51535   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-12-19 Blastula Embryo Embryo Imprecise All anatomical structures
43061 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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       149523181 122615352 117180131 97949905 6701107 SRX4168732 SRS3380685 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Multi-stage Embryo Embryo Imprecise All anatomical structures
43062 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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       442549747 365473385 344546726 292070542 61612 SRX4168731 SRS3380685 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Multi-stage Embryo Embryo Imprecise All anatomical structures
43063 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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       1097921080 906895047 849908073 707369464 82804 SRX4168730 SRS3380690 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Multi-stage Embryo Embryo Imprecise All anatomical structures
43064 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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       4126007145 3372127203 3172182791 2661287884 20781169 SRX4168729 SRS3380690 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Multi-stage Embryo Embryo Imprecise All anatomical structures
43065 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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       2815354570 2322972018 2180978488 1817457488 2627316 SRX4168728 SRS3380690 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Multi-stage Embryo Embryo Imprecise All anatomical structures
43066 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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       2428266964 2007082407 1885147455 1568726692 2776614 SRX4168727 SRS3380690 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Multi-stage Embryo Embryo Imprecise All anatomical structures
43067 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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       168630291 138451887 131779810 108186590 7520990 SRX4168726 SRS3380690 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Multi-stage Embryo Embryo Imprecise All anatomical structures
43068 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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       481887814 398331513 374271346 310815367 65276 SRX4168725 SRS3380690 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Multi-stage Embryo Embryo Imprecise All anatomical structures
43069 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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       2711637569 2235324807 2105535243 1791610098 1770467 SRX4168724 SRS3380685 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Multi-stage Embryo Embryo Imprecise All anatomical structures
43070 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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       2378019627 1963788516 1851111018 1572409542 3404749 SRX4168723 SRS3380685 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 1e-05   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Multi-stage Embryo Embryo Imprecise All anatomical structures
43071 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.       Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2 Raw multiplex: dmsseq AG01273;dmsseq AG01274   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                 Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2 AG01273.4;AG01274.4 AG01273.4;AG01274.4 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       2401597632 1861527917 1834777254 1415956870 757367 SRX4168722 SRS3380686 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Cleavage Embryo Embryo Imprecise All anatomical structures
43072 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.       Raw multiplex: RPF patA WT 64c RPF B1;RPF patA WT 64c RPF B2 Raw multiplex: ribo seq pata AG01409;ribo seq pata AG01410   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                 Raw multiplex: RPF patA WT 64c RPF B1;RPF patA WT 64c RPF B2 AG01409.1;AG01410.1 AG01409.1;AG01410.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       1280812305 1385761238 1441128504 836702863 355198 SRX4168721 SRS3380689 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43073 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       2850888928 3075001734 3215965099 1852417694 798089 SRX4168720 SRS3380688 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Cleavage Embryo Embryo Imprecise All anatomical structures
43074 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.       Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2 Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       146192524 109441919 103882304 87445288 29913 SRX4168719 SRS3380687 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 2e-05   1e-05   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43075 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.       Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2 Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       146683880 109166579 104154702 87473352 6979 SRX4168718 SRS3380687 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0023   0.00034   0.99326   0.57567   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43076 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.       Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2 Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       1552060471 1156267615 1104246757 927209997 504336 SRX4168717 SRS3380687 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.00235   0.00026   0.99379   0.60051   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Cleavage Embryo Embryo Imprecise All anatomical structures
43077 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.       Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2 Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       2212424663 1653496002 1573846163 1336100302 555906 SRX4168716 SRS3380687 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 3e-05   2e-05   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43078 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       517196379 393268952 372639155 310521534 106368 SRX4168715 SRS3380683 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 2e-05   0.0   0.99997   1.0   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43079 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       411772190 312434121 297408612 246654231 57834 SRX4168714 SRS3380683 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 1e-05   0.0   0.99997   0.0   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43080 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       373090462 283151050 269811169 223419849 119658 SRX4168713 SRS3380683 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.00222   0.0002   0.99362   0.55643   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Cleavage Embryo Embryo Imprecise All anatomical structures
43081 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.       Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2 Raw multiplex: dmsseq AG01273;dmsseq AG01274   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                 Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2 AG01273.3;AG01274.3 AG01273.3;AG01274.3 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       278837606 213606139 214029888 175477675 64716 SRX4168712 SRS3380686 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 6e-05   4e-05   0.99995   1.0   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43082 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.       Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2 Raw multiplex: dmsseq AG01273;dmsseq AG01274   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                 Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2 AG01273.2;AG01274.2 AG01273.2;AG01274.2 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       832670351 647746556 639758530 494461931 226688 SRX4168711 SRS3380686 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 5e-05   2e-05   0.99993   0.0   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43083 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.       Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1 Raw multiplex: dmsseq AG01269;dmsseq AG01270   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                 Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1 AG01269.4;AG01270.4 AG01269.4;AG01270.4 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       1100987855 897481291 850509260 655386223 151171 SRX4168710 SRS3380684 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.00251   0.00024   0.99334   0.49363   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Undetermined Embryo Embryo Imprecise All anatomical structures
43084 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.       Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1 Raw multiplex: dmsseq AG01269;dmsseq AG01270   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                 Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1 AG01269.3;AG01270.3 AG01269.3;AG01270.3 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       486730101 387546602 372319444 287072948 91389 SRX4168709 SRS3380684 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 4e-05   2e-05   0.99997   1.0   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Undetermined Embryo Embryo Imprecise All anatomical structures
43085 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.       Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2 Raw multiplex: dmsseq AG01273;dmsseq AG01274   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                 Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2 AG01273.1;AG01274.1 AG01273.1;AG01274.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       900945260 699348182 689446355 529699985 328786 SRX4168708 SRS3380686 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43086 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.       Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1 Raw multiplex: dmsseq AG01269;dmsseq AG01270   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                 Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1 AG01269.5;AG01270.5 AG01269.5;AG01270.5 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       3525623658 2869684594 2708534500 2083102664 159660 SRX4168707 SRS3380684 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Undetermined Embryo Embryo Imprecise All anatomical structures
43087 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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       1565087315 1292145008 1214936605 1030712352 121696 SRX4168706 SRS3380685 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 2e-05   1e-05   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Multi-stage Embryo Embryo Imprecise All anatomical structures
43088 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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       3451642355 2826476753 2670179644 2277897894 19534298 SRX4168705 SRS3380685 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Multi-stage Embryo Embryo Imprecise All anatomical structures
43089 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.       Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1 Raw multiplex: dmsseq AG01269;dmsseq AG01270   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                 Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1 AG01269.2;AG01270.2 AG01269.2;AG01270.2 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       1370691469 1101595011 1048719303 796936406 481019 SRX4168704 SRS3380684 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 1e-05   0.0   0.99997   0.0   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Undetermined Embryo Embryo Imprecise All anatomical structures
43090 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.       Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1 Raw multiplex: dmsseq AG01269;dmsseq AG01270   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                 Raw multiplex: DMS Seq IVT 64c B2;DMS Seq IVT 64c B1 AG01269.1;AG01270.1 AG01269.1;AG01270.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       1030573532 829398246 789085434 598013908 334400 SRX4168703 SRS3380684 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Undetermined Embryo Embryo Imprecise All anatomical structures
43091 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       2738474380 2086110939 1986494866 1661471870 796169 SRX4168702 SRS3380683 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 3e-05   2e-05   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Cleavage Embryo Embryo Imprecise All anatomical structures
43092 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.       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   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                 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     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       424319849 318879376 308835829 264971153 94465 SRX4168701 SRS3380683 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 9e-05   5e-05   0.99995   0.2   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Cleavage Embryo Embryo Imprecise All anatomical structures
43093 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.       miniRESA 6h a Am pA RNA B1 miniresa AG01714   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                 miniRESA 6h a Am pA RNA B1 AG01714.1 AG01714.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       71973779 48927629 51913512 91079622 6034 SRX3058793 SRS2404523 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.9163   3e-05   0.99833   0.61085   76   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Gastrula Embryo Embryo Imprecise All anatomical structures
43094 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.       miniRESA 6h a Am pA RNA B2 miniresa AG01715   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                 miniRESA 6h a Am pA RNA B2 AG01715.1 AG01715.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       63827548 43163354 46127646 80731865 60563 SRX3058792 SRS2404525 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.92571   3e-05   0.99809   0.62106   76   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Gastrula Embryo Embryo Imprecise All anatomical structures
43095 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.       miniRESA 2h pA RNA B1 miniresa AG01710   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                 miniRESA 2h pA RNA B1 AG01710.1 AG01710.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       63902747 43772893 46507615 81990822 4511 SRX3058791 SRS2404524 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.92111   4e-05   0.99799   0.56316   76   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Undetermined Embryo Embryo Imprecise All anatomical structures
43096 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.       miniRESA 2h pA RNA B2 miniresa AG01711   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                 miniRESA 2h pA RNA B2 AG01711.1 AG01711.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       61341697 41846683 44622362 78273216 5402 SRX3058790 SRS2404526 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.91845   1e-05   0.99797   0.60522   76   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Undetermined Embryo Embryo Imprecise All anatomical structures
43097 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.       miniRESA 6h pA RNA B1 miniresa AG01712   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                 miniRESA 6h pA RNA B1 AG01712.1 AG01712.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       67604374 45731516 48975112 85491937 5777 SRX3058789 SRS2404529 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.91668   4e-05   0.99837   0.57941   76   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Gastrula Embryo Embryo Imprecise All anatomical structures
43098 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.       miniRESA 6h pA RNA B2 miniresa AG01713   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                 miniRESA 6h pA RNA B2 AG01713.1 AG01713.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       86391705 58569607 62248447 107120293 7696 SRX3058788 SRS2404527 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.88475   1e-05   0.99845   0.62559   76   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Gastrula Embryo Embryo Imprecise All anatomical structures
43099 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.       mRNA Seq R0 patA WT 64c PatA RPF input B2 mrna seq pata AG01431   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                 mRNA Seq R0 patA WT 64c PatA RPF input B2 AG01431.1 AG01431.1 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       188726598 276745094 258235229 211815415 58488 SRX3058787 SRS2404528 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.89193   0.09644   0.7849   0.69832   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43100 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.       mRNA Seq R0 patA WT 64c PatA RPF input B2 mrna seq pata AG01431   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                 mRNA Seq R0 patA WT 64c PatA RPF input B2 AG01431.2 AG01431.2 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       541016830 720948568 664552003 623742439 275688 SRX3058786 SRS2404528 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.90466   0.10321   0.77595   0.60561   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43101 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.       mRNA Seq R0 patA WT 64c RPF input B1 mrna seq pata AG01432   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                 mRNA Seq R0 patA WT 64c RPF input B1 AG01432.1 AG01432.1 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       663756831 716464328 666812843 749363967 46731 SRX3058785 SRS2404530 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.85828   0.09273   0.75534   0.50507   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43102 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.       mRNA Seq R0 patA WT 64c RPF input B2 mrna seq pata AG01433   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                 mRNA Seq R0 patA WT 64c RPF input B2 AG01433.1 AG01433.1 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       715292036 869176418 807214698 816945712 53668 SRX3058784 SRS2404531 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.85439   0.09801   0.76597   0.58538   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43103 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.       DMS Seq WT 64c DMScontrol in vitro dmsseq AG00876   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                 DMS Seq WT 64c DMScontrol in vitro AG00876.2 AG00876.2 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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       37323535 39047425 34144869 28873865 6162 SRX3058783 SRS2404532 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.00316   0.00094   0.99318   0.54676   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43104 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.       DMS Seq WT 64c DMScontrol in vitro dmsseq AG00876   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                 DMS Seq WT 64c DMScontrol in vitro AG00876.1 AG00876.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       6246268 6429695 5629550 4937550 1309 SRX3058782 SRS2404532 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.02737   0.00562   0.96288   0.52983   76   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43105 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.       DMS Seq WT shield in vivo dmsseq AG01044   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                 DMS Seq WT shield in vivo AG01044.6 AG01044.6 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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     95827007 78301278 87345623 90923434 1895 SRX3058773 SRS2404537 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.57991   0.14096   0.78833   0.59313   19   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Gastrula Embryo Embryo Imprecise All anatomical structures
43106 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.       DMS Seq WT shield in vivo dmsseq AG01044   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                 DMS Seq WT shield in vivo AG01044.5 AG01044.5 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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     365900523 297605434 332516082 349160736 106002 SRX3058772 SRS2404537 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.58577   0.1419   0.7875   0.55349   34   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Gastrula Embryo Embryo Imprecise All anatomical structures
43107 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.       DMS Seq WT shield in vivo dmsseq AG01044   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                 DMS Seq WT shield in vivo AG01044.4 AG01044.4 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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     247816262 203789970 226994244 235814929 13134 SRX3058771 SRS2404537 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.58479   0.14134   0.7895   0.58758   17   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Gastrula Embryo Embryo Imprecise All anatomical structures
43108 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.       DMS Seq WT shield in vivo dmsseq AG01044   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                 DMS Seq WT shield in vivo AG01044.3 AG01044.3 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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     213097014 176081523 196161554 203036893 2232 SRX3058770 SRS2404537 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.58292   0.13842   0.78975   0.59022   16   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Gastrula Embryo Embryo Imprecise All anatomical structures
43109 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.       DMS Seq WT shield in vivo dmsseq AG01044   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                 DMS Seq WT shield in vivo AG01044.2 AG01044.2 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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     14492308 11955609 13424134 13741847 2642 SRX3058769 SRS2404537 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.56568   0.13601   0.79101   0.59727   26   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Gastrula Embryo Embryo Imprecise All anatomical structures
43110 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.       DMS Seq WT shield in vivo dmsseq AG01044   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                 DMS Seq WT shield in vivo AG01044.1 AG01044.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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     42428242 35110921 39122952 40378347 667 SRX3058768 SRS2404537 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.58493   0.13991   0.78735   0.59014   15   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Gastrula Embryo Embryo Imprecise All anatomical structures
43111 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.       DMS Seq WT sphere in vivo dmsseq AG01043   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                 DMS Seq WT sphere in vivo AG01043.6 AG01043.6 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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     66848740 56927652 60996703 60816631 1362 SRX3058767 SRS2404538 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.62265   0.12438   0.7696   0.59474   32   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Blastula Embryo Embryo Imprecise All anatomical structures
43112 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.       DMS Seq WT sphere in vivo dmsseq AG01043   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                 DMS Seq WT sphere in vivo AG01043.5 AG01043.5 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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     254864411 216185186 231676738 232716892 72995 SRX3058766 SRS2404538 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.6326   0.12713   0.76739   0.59812   27   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Blastula Embryo Embryo Imprecise All anatomical structures
43113 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.       DMS Seq WT sphere in vivo dmsseq AG01043   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                 DMS Seq WT sphere in vivo AG01043.4 AG01043.4 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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     172078766 147459021 157655737 156729321 9341 SRX3058765 SRS2404538 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.62892   0.12689   0.76915   0.59625   19   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Blastula Embryo Embryo Imprecise All anatomical structures
43114 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.       DMS Seq WT sphere in vivo dmsseq AG01043   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                 DMS Seq WT sphere in vivo AG01043.3 AG01043.3 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     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     147643154 127194084 135926112 134737007 1549 SRX3058764 SRS2404538 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.63069   0.12544   0.76781   0.60018   26   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Blastula Embryo Embryo Imprecise All anatomical structures
43115 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.       mRNA Seq R0 patA WT 64c PatA RPF input B1 mrna seq pata AG01430   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                 mRNA Seq R0 patA WT 64c PatA RPF input B1 AG01430.2 AG01430.2 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       672361176 875054552 808035984 777238497 338351 SRX3058763 SRS2404539 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.88898   0.09238   0.77234   0.6234   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43116 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.       mRNA Seq R0 patA WT 64c PatA RPF input B1 mrna seq pata AG01430   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                 mRNA Seq R0 patA WT 64c PatA RPF input B1 AG01430.1 AG01430.1 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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       187456862 260421633 242938837 207239930 57462 SRX3058762 SRS2404539 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.87315   0.08685   0.78117   0.65305   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2017-08-03 Cleavage Embryo Embryo Imprecise All anatomical structures
43117 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.       DMS Seq PatA WT 64c PatA DMS B2 dmsseq pata AG01429   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                 DMS Seq PatA WT 64c PatA DMS B2 AG01429.1 AG01429.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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     53713978 42339303 46822608 50276290 21 SRX3058761 SRS2404540 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.69688   0.0423   0.76621   0.51286   37   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43118 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.       DMS Seq PatA WT 64c PatA DMS B1 dmsseq pata AG01428   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                 DMS Seq PatA WT 64c PatA DMS B1 AG01428.5 AG01428.5 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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     427869397 311916291 327280051 404336571 12808 SRX3058760 SRS2404541 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.69068   0.05351   0.76625   0.51244   19   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43119 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.       DMS Seq PatA WT 64c PatA DMS B1 dmsseq pata AG01428   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                 DMS Seq PatA WT 64c PatA DMS B1 AG01428.4 AG01428.4 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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     60934366 43916600 46106309 57368748 751 SRX3058759 SRS2404541 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.68998   0.05396   0.76374   0.51059   17   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43120 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.       DMS Seq PatA WT 64c PatA DMS B1 dmsseq pata AG01428   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                 DMS Seq PatA WT 64c PatA DMS B1 AG01428.3 AG01428.3 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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     58823768 42490237 44567988 55298599 2444 SRX3058758 SRS2404541 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.6871   0.05281   0.76575   0.51538   30   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43121 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.       DMS Seq PatA WT 64c PatA DMS B2 dmsseq pata AG01429   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                 DMS Seq PatA WT 64c PatA DMS B2 AG01429.5 AG01429.5 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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     286439080 223476222 247260097 268171035 9209 SRX3058757 SRS2404540 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.69958   0.04484   0.76558   0.51603   29   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43122 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.       DMS Seq PatA WT 64c PatA DMS B2 dmsseq pata AG01429   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                 DMS Seq PatA WT 64c PatA DMS B2 AG01429.4 AG01429.4 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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     40943195 31523692 34943324 38167309 542 SRX3058756 SRS2404540 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.70235   0.04557   0.76341   0.5093   38   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43123 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.       DMS Seq PatA WT 64c PatA DMS B2 dmsseq pata AG01429   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                 DMS Seq PatA WT 64c PatA DMS B2 AG01429.3 AG01429.3 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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     39343164 30378209 33656711 36642421 1768 SRX3058755 SRS2404540 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.69621   0.04502   0.764   0.51161   28   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43124 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.       DMS Seq PatA WT 64c PatA DMS B2 dmsseq pata AG01429   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                 DMS Seq PatA WT 64c PatA DMS B2 AG01429.2 AG01429.2 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     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     43541418 33799983 37361242 40698001 0 SRX3058754 SRS2404540 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.70153   0.04589   0.76495   0.51164   21   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;