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
10212,ERR6511331,ERX6138167,ERS7264190,ERP131213,PRJEB46978,Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159,Other,Nano3P seq is a simple and robust method to accurately estimate transcript levels  tail lengths and tail nucleotide composition information in full length individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,,Zebrafish Nano3P seq of PolyA selected sample biological replicate 1 including 4 hpf RNA,Zebrafish PolyA 4 hpf,SAMEA9541420,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541420|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish PolyA 4 hpf|common name:zebrafish|sample name:Zebrafish PolyA 4 hpf|scientific name:Danio rerio,,,,,,,,,MinION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5,cDNA8523612,Nano3P seq,Nano3P seq,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,OXFORD_NANOPORE,MinION,,ERP131213,MinION sequencing,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,zebrafish_polya_4hpf.tar.gz,nanopore,330562220.0,233101.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5,0:1418.11,A:86572446;C:74232962;G:69203462;T:100553350;N:0,1418,,,,86572446,74232962,69203462,100553350,0,ERX6138167,ERS7264190,ERA5757997,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),1,0.0,,0.0,,1.0,,,,1536,,T,,long read,ont,ont,full_length,poly_a,unknown,bulk,unknown,unknown,,Spain,2023-12-28,Blastula,Embryo,Undetermined,Embryo Imprecise
10213,ERR6511329,ERX6138165,ERS7264188,ERP131213,PRJEB46978,Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159,Other,Nano3P seq is a simple and robust method to accurately estimate transcript levels  tail lengths and tail nucleotide composition information in full length individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,,Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs,Zebrafish Ribodep Rep1,SAMEA9541418,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541418|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish Ribodep Rep1|common name:zebrafish|sample name:Zebrafish Ribodep Rep1|scientific name:Danio rerio,,,,,,,,,MinION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3,cDNA786327,Nano3P seq,Nano3P seq,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,OXFORD_NANOPORE,MinION,,ERP131213,MinION sequencing,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,zebrafish_ribodep_rep1.tar.gz,nanopore,1745399583.0,1644167.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3,0:1061.57,A:449704009;C:421915878;G:378879857;T:494899839;N:0,1061,,,,449704009,421915878,378879857,494899839,0,ERX6138165,ERS7264188,ERA5757997,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),1,0.01112,,0.0,,0.99997,,1.0,,546,,T,,long read,ont,ont,full_length,rrna_depletion,unknown,bulk,unknown,unknown,,Spain,2023-12-28,Multi-stage,Embryo,Undetermined,Embryo Imprecise
10215,ERR6511330,ERX6138166,ERS7264189,ERP131213,PRJEB46978,Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159,Other,Nano3P seq is a simple and robust method to accurately estimate transcript levels  tail lengths and tail nucleotide composition information in full length individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,,Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs,Zebrafish Ribodep Rep2,SAMEA9541419,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541419|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish Ribodep Rep2|common name:zebrafish|sample name:Zebrafish Ribodep Rep2|scientific name:Danio rerio,,,,,,,,,MinION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4,cDNA123791,Nano3P seq,Nano3P seq,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,OXFORD_NANOPORE,MinION,,ERP131213,MinION sequencing,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,zebrafish_ribodep_rep2.tar.gz,nanopore,2038398139.0,1955617.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4,0:1042.33,A:518369802;C:477535545;G:441294056;T:601198736;N:0,1042,,,,518369802,477535545,441294056,601198736,0,ERX6138166,ERS7264189,ERA5757997,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),,,,,,,,,,,,,,,ont,ont,full_length,rrna_depletion,unknown,bulk,unknown,unknown,,Spain,2023-12-28,Multi-stage,Embryo,Undetermined,Embryo Imprecise
41827,SRR5251446,SRX2557171,SRS1974564,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR139 B1,nicoli mutmir AG01645,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR139 B1,AG01645.1,AG01645.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01645.1_R1.fastq.gz,fastq,1574284140.0,20714265.0,AG01645.1 R1.fastq.gz,0:76,A:485471345;C:270854124;G:374164721;T:443766613;N:27337,76,,,,485471345,270854124,374164721,443766613,27337,SRX2557171,SRS1974564,SRA537606,Yale University|Genetics,Yale University,1,0.82142,,0.14068,,0.8002,,0.5444,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-27,Undetermined,Embryo,Endothelium,Cardiovascular System
41828,SRR5251445,SRX2557170,SRS1974563,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR139 B2,nicoli mutmir AG01646,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR139 B2,AG01646.1,AG01646.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01646.1_R1.fastq.gz,fastq,1484740104.0,19536054.0,AG01646.1 R1.fastq.gz,0:76,A:453388316;C:246477203;G:365031959;T:419816346;N:26280,76,,,,453388316,246477203,365031959,419816346,26280,SRX2557170,SRS1974563,SRA537606,Yale University|Genetics,Yale University,1,0.82649,,0.1897,,0.79862,,0.52759,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41829,SRR5251444,SRX2557169,SRS1974562,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR139 B3,nicoli mutmir AG01647,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR139 B3,AG01647.1,AG01647.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01647.1_R1.fastq.gz,fastq,881298660.0,11596035.0,AG01647.1 R1.fastq.gz,0:76,A:270675838;C:160127586;G:228157662;T:222301246;N:36328,76,,,,270675838,160127586,228157662,222301246,36328,SRX2557169,SRS1974562,SRA537606,Yale University|Genetics,Yale University,1,0.76133,,0.15034,,0.83341,,0.56596,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41830,SRR5251443,SRX2557168,SRS1974561,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR139 B1,nicoli mutmir AG01648,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR139 B1,AG01648.1,AG01648.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01648.1_R1.fastq.gz,fastq,637896880.0,8393380.0,AG01648.1 R1.fastq.gz,0:76,A:192829278;C:112701153;G:153321271;T:179019095;N:26083,76,,,,192829278,112701153,153321271,179019095,26083,SRX2557168,SRS1974561,SRA537606,Yale University|Genetics,Yale University,1,0.75971,,0.1181,,0.82171,,0.56797,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41831,SRR5251442,SRX2557167,SRS1974560,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR139 B2,nicoli mutmir AG01649,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR139 B2,AG01649.1,AG01649.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01649.1_R1.fastq.gz,fastq,849868328.0,11182478.0,AG01649.1 R1.fastq.gz,0:76,A:258225905;C:148467172;G:205165181;T:237974100;N:35970,76,,,,258225905,148467172,205165181,237974100,35970,SRX2557167,SRS1974560,SRA537606,Yale University|Genetics,Yale University,1,0.75096,,0.14506,,0.81507,,0.5545,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41832,SRR5251441,SRX2557166,SRS1974559,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR139 B3,nicoli mutmir AG01650,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR139 B3,AG01650.1,AG01650.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01650.1_R1.fastq.gz,fastq,998464668.0,13137693.0,AG01650.1 R1.fastq.gz,0:76,A:311526420;C:176545041;G:251852786;T:258497630;N:42791,76,,,,311526420,176545041,251852786,258497630,42791,SRX2557166,SRS1974559,SRA537606,Yale University|Genetics,Yale University,1,0.76479,,0.11192,,0.82674,,0.54621,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41833,SRR5251440,SRX2557165,SRS1974558,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR24 B1,nicoli mutmir AG01651,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR24 B1,AG01651.1,AG01651.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01651.1_R1.fastq.gz,fastq,570492252.0,7506477.0,AG01651.1 R1.fastq.gz,0:76,A:162512811;C:104071716;G:135730697;T:168149427;N:27601,76,,,,162512811,104071716,135730697,168149427,27601,SRX2557165,SRS1974558,SRA537606,Yale University|Genetics,Yale University,1,0.73988,,0.10157,,0.86647,,0.54252,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41834,SRR5251439,SRX2557164,SRS1974557,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR24 B2,nicoli mutmir AG01652,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR24 B2,AG01652.1,AG01652.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01652.1_R1.fastq.gz,fastq,1072886148.0,14116923.0,AG01652.1 R1.fastq.gz,0:76,A:338399596;C:192703439;G:242960887;T:298769761;N:52465,76,,,,338399596,192703439,242960887,298769761,52465,SRX2557164,SRS1974557,SRA537606,Yale University|Genetics,Yale University,1,0.76456,,0.11024,,0.89197,,0.59214,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41835,SRR5251438,SRX2557163,SRS1974556,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR24 B3,nicoli mutmir AG01653,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR24 B3,AG01653.1,AG01653.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01653.1_R1.fastq.gz,fastq,1016374144.0,13373344.0,AG01653.1 R1.fastq.gz,0:76,A:310958343;C:168702106;G:223420046;T:313241363;N:52286,76,,,,310958343,168702106,223420046,313241363,52286,SRX2557163,SRS1974556,SRA537606,Yale University|Genetics,Yale University,1,0.75735,,0.12224,,0.79756,,0.55136,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-02-13,Undetermined,Embryo,Endothelium,Cardiovascular System
41836,SRR5251437,SRX2557162,SRS1974555,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR24 B1,nicoli mutmir AG01654,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR24 B1,AG01654.1,AG01654.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01654.1_R1.fastq.gz,fastq,782170112.0,10291712.0,AG01654.1 R1.fastq.gz,0:76,A:238316720;C:132163709;G:179301544;T:232350598;N:37541,76,,,,238316720,132163709,179301544,232350598,37541,SRX2557162,SRS1974555,SRA537606,Yale University|Genetics,Yale University,1,0.7683,,0.10712,,0.80034,,0.55804,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41837,SRR5251436,SRX2557161,SRS1974554,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR24 B2,nicoli mutmir AG01655,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR24 B2,AG01655.1,AG01655.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01655.1_R1.fastq.gz,fastq,1053946340.0,13867715.0,AG01655.1 R1.fastq.gz,0:76,A:318351311;C:191163031;G:240348413;T:304030367;N:53218,76,,,,318351311,191163031,240348413,304030367,53218,SRX2557161,SRS1974554,SRA537606,Yale University|Genetics,Yale University,1,0.77588,,0.07983,,0.83934,,0.56228,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41838,SRR5251435,SRX2557160,SRS1974553,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR24 B3,nicoli mutmir AG01656,,strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR24 B3,AG01656.1,AG01656.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01656.1_R1.fastq.gz,fastq,1182467736.0,15558786.0,AG01656.1 R1.fastq.gz,0:76,A:344465226;C:204677242;G:269228338;T:364036735;N:60195,76,,,,344465226,204677242,269228338,364036735,60195,SRX2557160,SRS1974553,SRA537606,Yale University|Genetics,Yale University,1,0.78956,,0.13495,,0.81517,,0.56342,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-02-13,Undetermined,Embryo,Endothelium,Cardiovascular System
41839,SRR5251434,SRX2557159,SRS1974552,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR223 B1,nicoli mutmir AG01657,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR223 B1,AG01657.1,AG01657.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01657.1_R1.fastq.gz,fastq,536336712.0,7057062.0,AG01657.1 R1.fastq.gz,0:76,A:158301607;C:93070120;G:121382262;T:163555487;N:27236,76,,,,158301607,93070120,121382262,163555487,27236,SRX2557159,SRS1974552,SRA537606,Yale University|Genetics,Yale University,1,0.76425,,0.1278,,0.84222,,0.55305,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-02-13,Undetermined,Embryo,Endothelium,Cardiovascular System
41840,SRR5251433,SRX2557158,SRS1974551,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR223 B2,nicoli mutmir AG01658,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR223 B2,AG01658.1,AG01658.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01658.1_R1.fastq.gz,fastq,798581856.0,10507656.0,AG01658.1 R1.fastq.gz,0:76,A:241352089;C:134327379;G:183394123;T:239469845;N:38420,76,,,,241352089,134327379,183394123,239469845,38420,SRX2557158,SRS1974551,SRA537606,Yale University|Genetics,Yale University,1,0.76221,,0.13398,,0.82459,,0.55228,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41841,SRR5251432,SRX2557157,SRS1974550,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   WT miR223 B3,nicoli mutmir AG01659,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   WT miR223 B3,AG01659.1,AG01659.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01659.1_R1.fastq.gz,fastq,1093998948.0,14394723.0,AG01659.1 R1.fastq.gz,0:76,A:330741822;C:186325335;G:249557623;T:327320449;N:53719,76,,,,330741822,186325335,249557623,327320449,53719,SRX2557157,SRS1974550,SRA537606,Yale University|Genetics,Yale University,1,0.77108,,0.14674,,0.80955,,0.55819,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
41842,SRR5251431,SRX2557156,SRS1974549,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR223 B1,nicoli mutmir AG01660,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 223 ya304/ya304|molecule:mRNA|condition:miR 223|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR223 B1,AG01660.1,AG01660.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01660.1_R1.fastq.gz,fastq,849905492.0,11182967.0,AG01660.1 R1.fastq.gz,0:76,A:250953875;C:146191904;G:190040699;T:262674911;N:44103,76,,,,250953875,146191904,190040699,262674911,44103,SRX2557156,SRS1974549,SRA537606,Yale University|Genetics,Yale University,1,0.7687,,0.14192,,0.82842,,0.5344,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-02-13,Undetermined,Embryo,Endothelium,Cardiovascular System
41843,SRR5251430,SRX2557155,SRS1974548,SRP099466,PRJNA374579,microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos,PRJNA374579,Other,Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.,,,,QuantSeq mutant miRNAs   Mut miR223 B2,nicoli mutmir AG01661,,strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 223 ya304/ya304|molecule:mRNA|condition:miR 223|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,QuantSeq mutant miRNAs   Mut miR223 B2,AG01661.1,AG01661.1,1,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP099466,,,AG01661.1_R1.fastq.gz,fastq,840115400.0,11054150.0,AG01661.1 R1.fastq.gz,0:76,A:257057495;C:141775085;G:188281166;T:252960590;N:41064,76,,,,257057495,141775085,188281166,252960590,41064,SRX2557155,SRS1974548,SRA537606,Yale University|Genetics,Yale University,1,0.74292,,0.10759,,0.83615,,0.55136,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,lexogen,bulk,unknown,unknown,,United States,2017-03-28,Undetermined,Embryo,Endothelium,Cardiovascular System
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
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
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
43125,SRR5893092,SRX3058753,SRS2404538,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,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,AG01043.1,AG01043.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01043.1_R1.fastq.gz,fastq,108747256.0,4575669.0,AG01043.1 R1.fastq.gz,0:23.77 1:0,A:29414532;C:25366431;G:27139739;T:26826074;N:480,23,0,,,29414532,25366431,27139739,26826074,480,SRX3058753,SRS2404538,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.62913,,0.12566,,0.76946,,0.59653,,20,,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
43126,SRR5893093,SRX3058752,SRS2404538,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,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,AG01043.2,AG01043.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01043.2_R1.fastq.gz,fastq,37331204.0,1581621.0,AG01043.2 R1.fastq.gz,0:23.60 1:0,A:10098397;C:8686566;G:9362492;T:9181793;N:1956,23,0,,,10098397,8686566,9362492,9181793,1956,SRX3058752,SRS2404538,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.60497,,0.12042,,0.77114,,0.5559,,21,,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
43127,SRR5893094,SRX3058751,SRS2404542,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT 64c in vivo,dmsseq AG01042,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT 64c in vivo,AG01042.1,AG01042.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01042.1_R1.fastq.gz,fastq,126429566.0,5343149.0,AG01042.1 R1.fastq.gz,0:23.66 1:0,A:33794193;C:29213503;G:32293032;T:31128226;N:612,23,0,,,33794193,29213503,32293032,31128226,612,SRX3058751,SRS2404542,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.60436,,0.07589,,0.78179,,0.58081,,23,,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
43128,SRR5893095,SRX3058750,SRS2404542,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT 64c in vivo,dmsseq AG01042,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT 64c in vivo,AG01042.2,AG01042.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01042.2_R1.fastq.gz,fastq,43162881.0,1835075.0,AG01042.2 R1.fastq.gz,0:23.52 1:0,A:11533531;C:9954515;G:11073245;T:10599502;N:2088,23,0,,,11533531,9954515,11073245,10599502,2088,SRX3058750,SRS2404542,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.58191,,0.07361,,0.78255,,0.5884,,27,,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
43129,SRR5893096,SRX3058749,SRS2404532,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,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,AG00876.3,AG00876.3,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG00876.3_R1.fastq.gz,fastq,981554972.0,12915197.0,AG00876.3 R1.fastq.gz,0:76,A:261237433;C:277515571;G:240090014;T:202665429;N:46525,76,,,,261237433,277515571,240090014,202665429,46525,SRX3058749,SRS2404532,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,2e-05,,0.0,,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
43130,SRR5893097,SRX3058748,SRS2404532,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,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,AG00876.4,AG00876.4,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP114782,,,AG00876.4_R1.fastq.gz,fastq,662935688.0,8722838.0,AG00876.4 R1.fastq.gz,0:76,A:176751346;C:187148186;G:162147575;T:136873146;N:15435,76,,,,176751346,187148186,162147575,136873146,15435,SRX3058748,SRS2404532,SRA596275,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
43131,SRR5893098,SRX3058747,SRS2404542,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT 64c in vivo,dmsseq AG01042,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT 64c in vivo,AG01042.5,AG01042.5,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01042.5_R1.fastq.gz,fastq,1080031154.0,45488589.0,AG01042.5 R1.fastq.gz,0:23.74 1:0,A:290744683;C:247189003;G:273714462;T:268297982;N:85024,23,0,,,290744683,247189003,273714462,268297982,85024,SRX3058747,SRS2404542,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.60791,,0.07492,,0.77979,,0.58326,,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
43132,SRR5893099,SRX3058746,SRS2404542,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT 64c in vivo,dmsseq AG01042,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT 64c in vivo,AG01042.6,AG01042.6,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01042.6_R1.fastq.gz,fastq,283394970.0,12033965.0,AG01042.6 R1.fastq.gz,0:23.55 1:0,A:76195456;C:65114236;G:72044677;T:70039067;N:1534,23,0,,,76195456,65114236,72044677,70039067,1534,SRX3058746,SRS2404542,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.59876,,0.07667,,0.78135,,0.58397,,33,,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
43133,SRR5893100,SRX3058745,SRS2404542,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT 64c in vivo,dmsseq AG01042,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT 64c in vivo,AG01042.3,AG01042.3,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01042.3_R1.fastq.gz,fastq,635217690.0,26879456.0,AG01042.3 R1.fastq.gz,0:23.63 1:0,A:169915710;C:146718321;G:161940079;T:156641690;N:1890,23,0,,,169915710,146718321,161940079,156641690,1890,SRX3058745,SRS2404542,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.60186,,0.07604,,0.78186,,0.58928,,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
43134,SRR5893101,SRX3058744,SRS2404542,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT 64c in vivo,dmsseq AG01042,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT 64c in vivo,AG01042.4,AG01042.4,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01042.4_R1.fastq.gz,fastq,737360617.0,31187809.0,AG01042.4 R1.fastq.gz,0:23.64 1:0,A:197816552;C:169921394;G:187620043;T:181992000;N:10628,23,0,,,197816552,169921394,187620043,181992000,10628,SRX3058744,SRS2404542,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.60088,,0.07706,,0.78046,,0.547,,15,,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
43135,SRR5893102,SRX3058743,SRS2404543,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT shield in vivo,dmsseq AG01047,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT shield in vivo,AG01047.3,AG01047.3,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01047.3_R1.fastq.gz,fastq,688382781.0,30034225.0,AG01047.3 R1.fastq.gz,0:22.92 1:0,A:189019980;C:152064230;G:163028336;T:184268177;N:2058,22,0,,,189019980,152064230,163028336,184268177,2058,SRX3058743,SRS2404543,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.57527,,0.14405,,0.7892,,0.59515,,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
43136,SRR5893103,SRX3058742,SRS2404543,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT shield in vivo,dmsseq AG01047,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT shield in vivo,AG01047.4,AG01047.4,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01047.4_R1.fastq.gz,fastq,786863431.0,34313776.0,AG01047.4 R1.fastq.gz,0:22.93 1:0,A:216579236;C:173455382;G:185880723;T:210944466;N:3624,22,0,,,216579236,173455382,185880723,210944466,3624,SRX3058742,SRS2404543,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.57576,,0.14501,,0.79026,,0.5962,,25,,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
43137,SRR5893104,SRX3058741,SRS2404544,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT 64c in vivo,dmsseq AG01046,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT 64c in vivo,AG01046.1,AG01046.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01046.1_R1.fastq.gz,fastq,104571264.0,4565699.0,AG01046.1 R1.fastq.gz,0:22.90 1:0,A:26920338;C:24177052;G:26506298;T:26967196;N:380,22,0,,,26920338,24177052,26506298,26967196,380,SRX3058741,SRS2404544,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.5641,,0.06574,,0.78437,,0.58268,,15,,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
43138,SRR5893105,SRX3058740,SRS2404544,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT 64c in vivo,dmsseq AG01046,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT 64c in vivo,AG01046.2,AG01046.2,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01046.2_R1.fastq.gz,fastq,34508189.0,1516870.0,AG01046.2 R1.fastq.gz,0:22.75 1:0,A:8891670;C:7954125;G:8796911;T:8864593;N:890,22,0,,,8891670,7954125,8796911,8864593,890,SRX3058740,SRS2404544,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.54153,,0.06305,,0.7852,,0.5792,,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
43139,SRR5893106,SRX3058739,SRS2404544,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT 64c in vivo,dmsseq AG01046,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT 64c in vivo,AG01046.3,AG01046.3,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01046.3_R1.fastq.gz,fastq,559711334.0,24457578.0,AG01046.3 R1.fastq.gz,0:22.88 1:0,A:144168923;C:129246711;G:141668875;T:144625154;N:1671,22,0,,,144168923,129246711,141668875,144625154,1671,SRX3058739,SRS2404544,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.56488,,0.06449,,0.7838,,0.57611,,20,,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
43140,SRR5893107,SRX3058738,SRS2404544,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT 64c in vivo,dmsseq AG01046,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT 64c in vivo,AG01046.4,AG01046.4,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01046.4_R1.fastq.gz,fastq,639006387.0,27909373.0,AG01046.4 R1.fastq.gz,0:22.90 1:0,A:165043321;C:147246240;G:161359572;T:165354476;N:2778,22,0,,,165043321,147246240,161359572,165354476,2778,SRX3058738,SRS2404544,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.56251,,0.06604,,0.78417,,0.57986,,18,,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
43141,SRR5893108,SRX3058737,SRS2404544,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT 64c in vivo,dmsseq AG01046,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT 64c in vivo,AG01046.5,AG01046.5,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01046.5_R1.fastq.gz,fastq,810814539.0,35324852.0,AG01046.5 R1.fastq.gz,0:22.95 1:0,A:209392559;C:186085613;G:205018734;T:210262020;N:55613,22,0,,,209392559,186085613,205018734,210262020,55613,SRX3058737,SRS2404544,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.57046,,0.06498,,0.78423,,0.5699,,22,,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
43142,SRR5893109,SRX3058736,SRS2404544,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT 64c in vivo,dmsseq AG01046,,strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT 64c in vivo,AG01046.6,AG01046.6,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01046.6_R1.fastq.gz,fastq,364856161.0,16004319.0,AG01046.6 R1.fastq.gz,0:22.80 1:0,A:94562115;C:83891926;G:92182690;T:94217438;N:1992,22,0,,,94562115,83891926,92182690,94217438,1992,SRX3058736,SRS2404544,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.56018,,0.06351,,0.78421,,0.58178,,15,,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
43143,SRR5893110,SRX3058735,SRS2404543,SRP114782,PRJNA397065,mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis,PRJNA397065,Other,RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.,,,,DMS Seq   WT shield in vivo,dmsseq AG01047,,strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:16|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,DMS Seq   WT shield in vivo,AG01047.1,AG01047.1,RNA,,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP114782,,,AG01047.1_R1.fastq.gz,fastq,128687784.0,5609452.0,AG01047.1 R1.fastq.gz,0:22.94 1:0,A:35296614;C:28459568;G:30549212;T:34381876;N:514,22,0,,,35296614,28459568,30549212,34381876,514,SRX3058735,SRS2404543,SRA596275,Yale_Giraldez|Genetics,Yale_Giraldez_Group,1,0.5755,,0.144,,0.7907,,0.59285,,22,,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