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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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